classes/config.template.php

@@ -1,4 +1,3 @@
-
 <?php
 declare(strict_types=1);
 
@@ -56,15 +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
@@ -81,6 +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');
 
@@ -127,6 +135,7 @@ ENV::setPub('SRI', 'sha384');
  * Tech support
  */
 
+ /*
 $TechSupport = [
   'Email' => 'help@biotorrents.de',
   'Subject' => '[TxID '.strtoupper(bin2hex(random_bytes(2))).'] Specific subject line with TxID intact',
@@ -136,6 +145,7 @@ ENV::setPub(
     'HELP',
     $ENV->convert($TechSupport)
 );
+*/
 
 
 /**
@@ -380,7 +390,8 @@ ENV::setPub('FEATURE_SEND_EMAIL', true);
 # (should only be used for initial setup)
 ENV::setPub('FEATURE_SET_ENC_KEY_PUBLIC', false);
 
-# Attempt to support the Seqhash algorithm
+# Attempt to support the BioPHP library
+# https://packagist.org/packages/biotorrents/biophp
 # https://blog.libredna.org/post/seqhash/
 ENV::setPub('FEATURE_BIOPHP', true);
 
@@ -831,6 +842,9 @@ $DB = [
     'version' => ['name' => 'Version', 'desc' => 'Start with 0.1.0', 'note' => 'Please see <a href="https://semver.org" target="_blank">Semantic Versioning</a>'],
     'license' => ['name' => 'License', 'desc' => '', 'note' => 'Please see <a href="http://www.dcc.ac.uk/resources/how-guides/license-research-data" target="_blank">How to License Research Data</a>'],
     'mirrors' => ['name' => 'Mirrors', 'desc' => 'Up to two FTP/HTTP addresses that either point directly to a file, or for multi-file torrents, to the enclosing folder'],
+
+    # Original fields
+    'seqhash' => ['name' => 'Seqhash', 'desc' => 'Sample genome sequence in FASTA format (GenBank pending)', 'note' => 'Please see <a href="https://blog.libredna.org/post/seqhash/" target="_blank">The Seqhash Algorithm</a>'],
 ];
 ENV::setPub(
     'DB',
@@ -971,10 +985,23 @@ $META = [
         'Plain' => [
             'CSV'   => ['csv'], # 3
             'JSON'  => ['json'], # 3
-            'Text'  => ['txt'], # 3
+            'Text'  => ['txt', 'asc'], # 3
             'XML'   => ['xml'], # etc.
         ],
 
+        /**
+         * 2.
+         * Databases
+         */
+        'Databases' => [
+            'MS SQL'   => ['mdf', 'ndf', 'ldf'],
+            'MySQL'   => ['sql', 'mysql'],
+            'Oracle' => ['dbf', 'ora', 'oraenv'],
+            'IBM Db2' => ['ixf', 'del', 'cursor'],
+            'Postgres' => ['sql']
+        ],
+
+
         /**
          * 2.
          * Archives
@@ -1330,16 +1357,11 @@ $CATS = [
         'Icon' => "$CatIcons/sequences.png",
         'Description' => "For data that's ACGT, ACGU, amino acid letters on disk.",
         'Platforms' => $ENV->META->Platforms->Sequences,
-        'Formats' => array_merge([
-            /*
-            'Sequences' => $ENV->META->Formats->Sequences,
-            'Proteins' => $ENV->META->Formats->Proteins,
-            'Plain' => $ENV->META->Formats->Plain,
-            */
+        'Formats' => [
             $ENV->META->Formats->Sequences,
             $ENV->META->Formats->Proteins,
             $ENV->META->Formats->Plain,
-        ]),
+        ],
     ],
 
     2 => [
@@ -1349,9 +1371,9 @@ $CATS = [
         'Description' => 'For pathway and regulatory network data, structured taxonomies, etc.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1362,9 +1384,9 @@ $CATS = [
         'Description' => 'For data that examines one facet broadly, not one subject deeply.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1375,9 +1397,9 @@ $CATS = [
         'Description' => "For structured data (XML, etc.) that describes the subject's orientation in space.",
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1388,9 +1410,9 @@ $CATS = [
         'Description' => 'For data that describes observations over time and/or space.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1401,9 +1423,9 @@ $CATS = [
         'Description' => 'For data that describes recurring structures in nature such as common pathways or motifs in the proteome or metabolome.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1414,9 +1436,9 @@ $CATS = [
         'Description' => 'For data that records experimental control behavior, checks readings against known physical constants, tracks the thermodynamic limits of reactions, etc.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'GraphXml' => $ENV->META->Formats->GraphXml,
-            'GraphTxt' => $ENV->META->Formats->GraphTxt,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->GraphXml,
+            $ENV->META->Formats->GraphTxt,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1427,9 +1449,8 @@ $CATS = [
         'Description' => 'For data you can look at!',
         'Platforms' => $ENV->META->Platforms->Images,
         'Formats' => [
-            'ImgRaster' => $ENV->META->Formats->ImgRaster,
-            'ImgVector' => $ENV->META->Formats->ImgVector,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->ImgRaster,
+            $ENV->META->Formats->ImgVector,
         ],
     ],
 
@@ -1440,11 +1461,10 @@ $CATS = [
         'Description' => "For data that's limited to specific locations or otherwise describes macroscopic space.",
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'MapRaster' => $ENV->META->Formats->MapRaster,
-            'MapVector' => $ENV->META->Formats->MapVector,
-            'ImgRaster' => $ENV->META->Formats->ImgRaster,
-            'ImgVector' => $ENV->META->Formats->ImgVector,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->MapRaster,
+            $ENV->META->Formats->MapVector,
+            $ENV->META->Formats->ImgRaster,
+            $ENV->META->Formats->ImgVector,
         ],
     ],
 
@@ -1455,11 +1475,10 @@ $CATS = [
         'Description' => 'For projections, simulations, and other hypothetical or computer-generated data.',
         'Platforms' => $ENV->META->Platforms->Graphs,
         'Formats' => [
-            'MapRaster' => $ENV->META->Formats->MapRaster,
-            'MapVector' => $ENV->META->Formats->MapVector,
-            'ImgRaster' => $ENV->META->Formats->ImgRaster,
-            'ImgVector' => $ENV->META->Formats->ImgVector,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->MapRaster,
+            $ENV->META->Formats->MapVector,
+            $ENV->META->Formats->ImgRaster,
+            $ENV->META->Formats->ImgVector,
         ],
     ],
 
@@ -1470,9 +1489,9 @@ $CATS = [
         'Description' => 'For documentation, software, disk images, and literature datasets.',
         'Platforms' => $ENV->META->Platforms->Documents,
         'Formats' => [
-            'BinDoc' => $ENV->META->Formats->BinDoc,
-            'CpuGen' => $ENV->META->Formats->CpuGen,
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->BinDoc,
+            $ENV->META->Formats->CpuGen,
+            $ENV->META->Formats->Plain,
         ],
     ],
 
@@ -1483,7 +1502,7 @@ $CATS = [
         'Description' => 'For raw reads and machine data of any category.',
         'Platforms' => $ENV->META->Platforms->Raw,
         'Formats' => [
-            'Plain' => $ENV->META->Formats->Plain,
+            $ENV->META->Formats->Plain,
         ],
     ],
 ];
@@ -1501,10 +1520,10 @@ ENV::setPub(
  */
 
 // resource_type://username:password@domain:port/path?query_string#anchor
-define('RESOURCE_REGEX', '(https?|ftps?):\/\/');
+define('RESOURCE_REGEX', '(https?|ftps?|dat|ipfs):\/\/');
 ENV::setPub(
     'RESOURCE_REGEX',
-    '(https?|ftps?):\/\/'
+    '(https?|ftps?|dat|ipfs):\/\/'
 );
 
 define('IP_REGEX', '(\d{1,3}\.){3}\d{1,3}');

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
+        )
+    );
 }
 
 /**

classes/validate.class.php

@@ -46,6 +46,34 @@
 
 class Validate
 {
+    /**
+     * mirrors
+     *
+     * @param string $String The raw textarea, e.g., from torrent_form.class.php
+     * @param string $Regex  The regex to test against, e.g., from $ENV
+     * @return array An array of unique values that match the regex
+     */
+    public function textarea2array(string $String, string $Regex)
+    {
+        $ENV = ENV::go();
+
+        $String = array_map(
+            'trim',
+            explode(
+                "\n",
+                $String
+            )
+        );
+        
+        return array_unique(
+            preg_grep(
+                "/^$Regex$/i",
+                $String
+            )
+        );
+    }
+
+    
     /**
      * title
      *
@@ -245,58 +273,6 @@ class Validate
     }
 
 
-    /**
-     * Make input
-     * https://www.w3schools.com/html/html_form_input_types.asp
-     *
-     * Generate a secure HTML input element.
-     * Takes $Type, $Name (also used for id), and $Classes.
-     * Outputs a hardened input with the requested attributes.
-     *
-     * todo: See if this could work, one ugly switch for all forms in sections/
-     */
-
-    public function MakeInput($Type = 'text', $Name = '', $Classes = [])
-    {
-        if (!is_str($Type) || !is_str($Name)) {
-            error('$Type and $Name must be strings');
-        }
-
-        # Intentionally double quoted PHP constructing $HTML
-        # <input type='text' id='title_jp' name='title_jp' class='one two'
-        $HTML  = "";
-        $HTML .= "<input type='$Type' id='$Name' name='$Name'";
-        $HTML .= (!empty($Classes)) ? " class='" . implode(' ', $Classes) . "'" : "";
-
-        /*
-        'button'
-        'checkbox'
-        'color'
-        'date'
-        'datetime-local'
-        'email'
-        'file'
-        'hidden'
-        'image'
-        'month'
-        'number'
-        'password'
-        'radio'
-        'range'
-        'reset'
-        'search'
-        'submit'
-        'tel'
-        'text'
-        'time'
-        'url'
-        'week'
-        */
-                
-        return;
-    }
-    
-
     /**
      * Legacy class
      */

composer.lock

@@ -776,16 +776,16 @@
         },
         {
             "name": "symfony/config",
-            "version": "v5.3.3",
+            "version": "v5.3.4",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/config.git",
-                "reference": "a69e0c55528b47df88d3c4067ddedf32d485d662"
+                "reference": "4268f3059c904c61636275182707f81645517a37"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/config/zipball/a69e0c55528b47df88d3c4067ddedf32d485d662",
-                "reference": "a69e0c55528b47df88d3c4067ddedf32d485d662",
+                "url": "https://api.github.com/repos/symfony/config/zipball/4268f3059c904c61636275182707f81645517a37",
+                "reference": "4268f3059c904c61636275182707f81645517a37",
                 "shasum": ""
             },
             "require": {
@@ -793,7 +793,7 @@
                 "symfony/deprecation-contracts": "^2.1",
                 "symfony/filesystem": "^4.4|^5.0",
                 "symfony/polyfill-ctype": "~1.8",
-                "symfony/polyfill-php80": "^1.15",
+                "symfony/polyfill-php80": "^1.16",
                 "symfony/polyfill-php81": "^1.22"
             },
             "conflict": {
@@ -835,7 +835,7 @@
             "description": "Helps you find, load, combine, autofill and validate configuration values of any kind",
             "homepage": "https://symfony.com",
             "support": {
-                "source": "https://github.com/symfony/config/tree/v5.3.3"
+                "source": "https://github.com/symfony/config/tree/v5.3.4"
             },
             "funding": [
                 {
@@ -851,20 +851,20 @@
                     "type": "tidelift"
                 }
             ],
-            "time": "2021-06-24T08:13:00+00:00"
+            "time": "2021-07-21T12:40:44+00:00"
         },
         {
             "name": "symfony/console",
-            "version": "v5.3.2",
+            "version": "v5.3.4",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/console.git",
-                "reference": "649730483885ff2ca99ca0560ef0e5f6b03f2ac1"
+                "reference": "ebd610dacd40d75b6a12bf64b5ccd494fc7d6ab1"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/console/zipball/649730483885ff2ca99ca0560ef0e5f6b03f2ac1",
-                "reference": "649730483885ff2ca99ca0560ef0e5f6b03f2ac1",
+                "url": "https://api.github.com/repos/symfony/console/zipball/ebd610dacd40d75b6a12bf64b5ccd494fc7d6ab1",
+                "reference": "ebd610dacd40d75b6a12bf64b5ccd494fc7d6ab1",
                 "shasum": ""
             },
             "require": {
@@ -872,11 +872,12 @@
                 "symfony/deprecation-contracts": "^2.1",
                 "symfony/polyfill-mbstring": "~1.0",
                 "symfony/polyfill-php73": "^1.8",
-                "symfony/polyfill-php80": "^1.15",
+                "symfony/polyfill-php80": "^1.16",
                 "symfony/service-contracts": "^1.1|^2",
                 "symfony/string": "^5.1"
             },
             "conflict": {
+                "psr/log": ">=3",
                 "symfony/dependency-injection": "<4.4",
                 "symfony/dotenv": "<5.1",
                 "symfony/event-dispatcher": "<4.4",
@@ -884,10 +885,10 @@
                 "symfony/process": "<4.4"
             },
             "provide": {
-                "psr/log-implementation": "1.0"
+                "psr/log-implementation": "1.0|2.0"
             },
             "require-dev": {
-                "psr/log": "~1.0",
+                "psr/log": "^1|^2",
                 "symfony/config": "^4.4|^5.0",
                 "symfony/dependency-injection": "^4.4|^5.0",
                 "symfony/event-dispatcher": "^4.4|^5.0",
@@ -933,7 +934,7 @@
                 "terminal"
             ],
             "support": {
-                "source": "https://github.com/symfony/console/tree/v5.3.2"
+                "source": "https://github.com/symfony/console/tree/v5.3.4"
             },
             "funding": [
                 {
@@ -949,7 +950,7 @@
                     "type": "tidelift"
                 }
             ],
-            "time": "2021-06-12T09:42:48+00:00"
+            "time": "2021-07-26T16:33:26+00:00"
         },
         {
             "name": "symfony/deprecation-contracts",
@@ -1020,21 +1021,22 @@
         },
         {
             "name": "symfony/filesystem",
-            "version": "v5.3.3",
+            "version": "v5.3.4",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/filesystem.git",
-                "reference": "19b71c8f313b411172dd5f470fd61f24466d79a9"
+                "reference": "343f4fe324383ca46792cae728a3b6e2f708fb32"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/filesystem/zipball/19b71c8f313b411172dd5f470fd61f24466d79a9",
-                "reference": "19b71c8f313b411172dd5f470fd61f24466d79a9",
+                "url": "https://api.github.com/repos/symfony/filesystem/zipball/343f4fe324383ca46792cae728a3b6e2f708fb32",
+                "reference": "343f4fe324383ca46792cae728a3b6e2f708fb32",
                 "shasum": ""
             },
             "require": {
                 "php": ">=7.2.5",
-                "symfony/polyfill-ctype": "~1.8"
+                "symfony/polyfill-ctype": "~1.8",
+                "symfony/polyfill-php80": "^1.16"
             },
             "type": "library",
             "autoload": {
@@ -1062,7 +1064,7 @@
             "description": "Provides basic utilities for the filesystem",
             "homepage": "https://symfony.com",
             "support": {
-                "source": "https://github.com/symfony/filesystem/tree/v5.3.3"
+                "source": "https://github.com/symfony/filesystem/tree/v5.3.4"
             },
             "funding": [
                 {
@@ -1078,7 +1080,7 @@
                     "type": "tidelift"
                 }
             ],
-            "time": "2021-06-30T07:27:52+00:00"
+            "time": "2021-07-21T12:40:44+00:00"
         },
         {
             "name": "symfony/polyfill-ctype",
@@ -3934,16 +3936,16 @@
         },
         {
             "name": "theseer/tokenizer",
-            "version": "1.2.0",
+            "version": "1.2.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/theseer/tokenizer.git",
-                "reference": "75a63c33a8577608444246075ea0af0d052e452a"
+                "reference": "34a41e998c2183e22995f158c581e7b5e755ab9e"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/theseer/tokenizer/zipball/75a63c33a8577608444246075ea0af0d052e452a",
-                "reference": "75a63c33a8577608444246075ea0af0d052e452a",
+                "url": "https://api.github.com/repos/theseer/tokenizer/zipball/34a41e998c2183e22995f158c581e7b5e755ab9e",
+                "reference": "34a41e998c2183e22995f158c581e7b5e755ab9e",
                 "shasum": ""
             },
             "require": {
@@ -3972,7 +3974,7 @@
             "description": "A small library for converting tokenized PHP source code into XML and potentially other formats",
             "support": {
                 "issues": "https://github.com/theseer/tokenizer/issues",
-                "source": "https://github.com/theseer/tokenizer/tree/master"
+                "source": "https://github.com/theseer/tokenizer/tree/1.2.1"
             },
             "funding": [
                 {
@@ -3980,7 +3982,7 @@
                     "type": "github"
                 }
             ],
-            "time": "2020-07-12T23:59:07+00:00"
+            "time": "2021-07-28T10:34:58+00:00"
         },
         {
             "name": "webmozart/assert",

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"

gazelle.sql

@@ -143,6 +143,20 @@ CREATE TABLE `badges` (
 ) ENGINE=InnoDB CHARSET=utf8mb4;
 
 
+-- 2021-07-28
+CREATE TABLE `bioinformatics` (
+  `id` int NOT NULL AUTO_INCREMENT,
+  `torrent_id` int NOT NULL,
+  `user_id` int NOT NULL,
+  `timestamp` datetime NOT NULL,
+  `name` varchar(255) DEFAULT NULL,
+  `seqhash` varchar(100) DEFAULT NULL,
+  `gc_content` tinyint DEFAULT NULL,
+  `monoisotopic_mass` double DEFAULT NULL,
+  PRIMARY KEY (`id`,`torrent_id`,`user_id`) 
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
+
+
 -- 2020-03-09
 CREATE TABLE `blog` (
   `ID` int unsigned NOT NULL AUTO_INCREMENT,
@@ -1241,23 +1255,14 @@ CREATE TABLE `torrents_recommended` (
 ) ENGINE=InnoDB CHARSET=utf8mb4;
 
 
-CREATE TABLE `torrents_doi` (
-  `ID` int NOT NULL AUTO_INCREMENT,
-  `TorrentID` int NOT NULL,
-  `UserID` int NOT NULL,
-  `Time` datetime,
-  `URI` varchar(255) NOT NULL,
-  PRIMARY KEY (`ID`,`GroupID`,`URI`)
-) ENGINE=InnoDB CHARSET=utf8mb4;
-
-
+-- 2021-07-28
 CREATE TABLE `torrents_mirrors` (
-  `ID` int NOT NULL AUTO_INCREMENT,
-  `GroupID` int NOT NULL,
-  `UserID` int NOT NULL,
-  `Time` datetime,
-  `URI` varchar(255) NOT NULL,
-  PRIMARY KEY (`ID`,`GroupID`,`URI`)
+  `id` int NOT NULL AUTO_INCREMENT,
+  `torrent_id` int NOT NULL,
+  `user_id` int NOT NULL,
+  `timestamp` datetime,
+  `uri` varchar(255) NOT NULL,
+  PRIMARY KEY (`id`,`torrent_id`,`uri`)
 ) ENGINE=InnoDB CHARSET=utf8mb4;
 
 

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/editgroup.php

@@ -43,14 +43,14 @@ list($title, $subject, $object, $Image, $Body, $picture, $description, $publishe
 
 $DB->prepare_query("
 SELECT
-  `ID`,
-  `UserID`,
-  `Time`,
-  `URI`
+  `id`,
+  `user_id`,
+  `timestamp`,
+  `doi`
 FROM
-  `torrents_doi`
+  `literature`
 WHERE
-  `TorrentID` = '$group_id'
+  `group_id` = '$group_id'
 ");
 $DB->exec_prepared_query();
 

sections/torrents/functions.php

@@ -58,14 +58,14 @@ function get_group_info($GroupID, $Return = true, $RevisionID = 0, $PersonalProp
         # Screenshots (Publications)
         $DB->query("
         SELECT
-          `ID`,
-          `UserID`,
-          `Time`,
-          `URI`
+          `id`,
+          `user_id`,
+          `timestamp`,
+          `doi`
         FROM
-          `torrents_doi`
+          `literature`
         WHERE
-          `TorrentID` = '$GroupID'
+          `group_id` = '$GroupID'
         ");
 
         if ($DB->has_results()) {
@@ -75,16 +75,17 @@ function get_group_info($GroupID, $Return = true, $RevisionID = 0, $PersonalProp
         }
 
         # Mirrors
+        # todo: Fix $GroupID
         $DB->query("
         SELECT
-          `ID`,
-          `UserID`,
-          `Time`,
-          `URI`
+          `id`,
+          `user_id`,
+          `timestamp`,
+          `uri`
         FROM
           `torrents_mirrors`
         WHERE
-          `GroupID` = '$GroupID'
+          `torrent_id` = '$GroupID'
         ");
   
         if ($DB->has_results()) {

sections/torrents/screenshotedit.php

@@ -36,12 +36,12 @@ if (count($Screenshots) > 10) {
 
 $DB->query("
 SELECT
-  `UserID`,
-  `URI`
+  `user_id`,
+  `doi`
 FROM
-  `torrents_doi`
+  `literature`
 WHERE
-  `TorrentID` = '$GroupID'
+  `group_id` = '$GroupID'
 ");
 
 // $Old is an array of the form URL => UserID where UserID is the ID of the User who originally uploaded that image.
@@ -81,9 +81,9 @@ if (!empty($Deleted)) {
         $DB->prepare_query("
         DELETE
         FROM
-          `torrents_doi`
+          `literature`
         WHERE
-          `URI` = '$ScreenDel'
+          `doi` = '$ScreenDel'
         ");
 
         foreach ($DeleteList as $ScreenDel) {
@@ -100,8 +100,8 @@ if (!empty($New)) {
     $Screenshot = '';
     $DB->prepare_query(
         "
-    INSERT INTO `torrents_doi`
-      (`TorrentID`, `UserID`, `Time`, `URI`)
+    INSERT INTO `literature`
+      (`group_id`, `user_id`, `timestamp`, `doi`)
     VALUES
       (?, ?, NOW(), ?)",
         $GroupID,

sections/upload/upload_handle.php

@@ -79,6 +79,7 @@ $Properties['GroupDescription'] = trim($_POST['album_desc']);
 $Properties['TorrentDescription'] = $_POST['release_desc'];
 $Properties['Screenshots'] = isset($_POST['screenshots']) ? $_POST['screenshots'] : '';
 $Properties['Mirrors'] = isset($_POST['mirrors']) ? $_POST['mirrors'] : '';
+$Properties['Seqhash'] = isset($_POST['seqhash']) ? $_POST['seqhash'] : '';
 
 if ($_POST['album_desc']) {
     $Properties['GroupDescription'] = trim($_POST['album_desc']);
@@ -209,7 +210,7 @@ if (!$_POST['groupid']) {
         '1',
         'inarray',
         'Please select a valid platform.',
-        array('inarray' => $ENV->flatten($ENV->META->Platforms))
+        array('inarray' => $ENV->META->Platforms)
     );
 
     /*
@@ -438,8 +439,8 @@ if ($T['GroupID']) {
     FROM
       `torrents_group`
     WHERE
-      `id` = $T[GroupID]
-    ");
+      `id` = ?
+    ", $T['GroupID']);
     $DB->exec_prepared_query();
 
     if ($DB->has_results()) {
@@ -516,7 +517,7 @@ if ((!isset($GroupID) || !$GroupID)) {
 
 if (!isset($GroupID) || !$GroupID) {
     // Create torrent group
-    $DB->prepare_query(
+    $DB->query(
         "
       INSERT INTO torrents_group
         (`category_id`, `title`, `subject`, `object`, `year`,
@@ -526,7 +527,7 @@ if (!isset($GroupID) || !$GroupID) {
         ( ?, ?, ?, ?, ?,
           ?, ?, ?, NOW(),
           ?, ? )",
-        $TypeID,
+        $T['CategoryID'],
         $T['Title'],
         $T['Title2'],
         $T['TitleJP'],
@@ -537,7 +538,6 @@ if (!isset($GroupID) || !$GroupID) {
         $Body,
         $T['Image']
     );
-    $DB->exec_prepared_query();
 
     $GroupID = $DB->inserted_id();
     foreach ($ArtistForm as $Num => $Artist) {
@@ -550,67 +550,33 @@ if (!isset($GroupID) || !$GroupID) {
     }
     $Cache->increment('stats_group_count');
 
-    // Add screenshots
-    // todo: Clear DB_MYSQL::exec_prepared_query() errors
-    $Screenshots = explode("\n", $T['Screenshots']);
-    $Screenshots = array_map('trim', $Screenshots);
-
-    $Screenshots = array_filter($Screenshots, function ($s) {
-        return preg_match('/^'.$ENV->DOI_REGEX.'$/i', $s);
-    });
-
-    $Screenshots = array_unique($Screenshots);
-    $Screenshots = array_slice($Screenshots, 0, 10);
-
-    # Add optional web seeds similar to screenshots
-    # Support an arbitrary and limited number of sources
-    $Mirrors = explode("\n", $T['Mirrors']);
-    $Mirrors = array_map('trim', $Mirrors);
-
-    $Mirrors = array_filter($Mirrors, function ($s) {
-        return preg_match('/^'.URL_REGEX.'$/i', $s);
-    });
-
-    $Mirrors = array_unique($Mirrors);
-    $Mirrors = array_slice($Mirrors, 0, 2);
-
-    # Downgrade TLS on resource URIs
-    # Required for BEP 19 compatibility
-    $Mirrors = str_ireplace('tps://', 'tp://', $Mirrors);
-
-    # Perform the DB inserts here
-    # Screenshots (Publications)
-    if (!empty($Screenshots)) {
-        $Screenshot = '';
-        $DB->prepare_query("
-          INSERT INTO torrents_doi
-            (TorrentID, UserID, Time, URI)
-          VALUES (?, ?, NOW(), ?)", $GroupID, $LoggedUser['ID'], $Screenshot);
-
-        foreach ($Screenshots as $Screenshot) {
-            $DB->exec_prepared_query();
-        }
-    }
 
-    # Mirrors
-    if (!empty($Mirrors)) {
-        $Mirror = '';
-        $DB->prepare_query("
-          INSERT INTO torrents_mirrors
-            (GroupID, UserID, Time, URI)
-          VALUES (?, ?, NOW(), ?)", $GroupID, $LoggedUser['ID'], $Mirror);
+    /**
+     * DOI numbers
+     *
+     * Add optional citation info.
+     * todo: Query Semantic Scholar in the scheduler.
+     * THESE ARE ASSOCIATED WITH TORRENT GROUPS.s
+     */
+    if (!empty($T['Screenshots'])) {
+        $Screenshots = $Validate->textarea2array($T['Screenshots'], $ENV->DOI_REGEX);
+        $Screenshots = array_slice($Screenshots, 0, 10);
 
-        foreach ($Mirrors as $Mirror) {
-            $DB->exec_prepared_query();
+        foreach ($Screenshots as $Screenshot) {
+            $DB->query("
+            INSERT INTO `literature`
+            (`group_id`, `user_id`, `timestamp`, `doi`)
+          VALUES (?, ?, NOW(), ?)", $GroupID, $LoggedUser['ID'], $Screenshot);
         }
     }
+}
 
-    # Main if/else
-} else {
+# Main if/else
+else {
     $DB->query("
       UPDATE torrents_group
-      SET Time = NOW()
-        WHERE ID = ?", $GroupID);
+      SET `timestamp` = NOW()
+        WHERE `id` = ?", $GroupID);
 
     $Cache->delete_value("torrent_group_$GroupID");
     $Cache->delete_value("torrents_details_$GroupID");
@@ -728,6 +694,77 @@ $TorrentID = $DB->inserted_id();
 $Cache->increment('stats_torrent_count');
 $Tor->Dec['comment'] = 'https://'.SITE_DOMAIN.'/torrents.php?torrentid='.$TorrentID;
 
+
+/**
+ * Mirrors
+ *
+ * Add optional web seeds and IPFS/Dat mirrors.
+ * Support an arbitrary and limited number of sources.
+ * THESE ARE ASSOCIATED WITH INDIVIDUAL TORRENTS.
+ */
+
+if (!empty($T['Mirrors'])) {
+    $Mirrors = $Validate->textarea2array($T['Mirrors'], $ENV->URL_REGEX);
+    $Screenshots = array_slice($Screenshots, 0, 5);
+
+    foreach ($Mirrors as $Mirror) {
+        $DB->query(
+            "
+        INSERT INTO `torrents_mirrors`
+          (`torrent_id`, `user_id`, `timestamp`, `uri`)
+        VALUES (?, ?, NOW(), ?)",
+            $TorrentID,
+            $LoggedUser['ID'],
+            $Mirror
+        );
+    }
+}
+
+
+/**
+ * Seqhash
+ *
+ * Elementary Seqhash support
+ */
+if ($ENV->FEATURE_BIOPHP && !empty($T['Seqhash'])) {
+    $BioIO = new \BioPHP\IO();
+    $BioSeqhash = new \BioPHP\Seqhash();
+
+    $Parsed = $BioIO->readFasta($T['Seqhash']);
+    foreach ($Parsed as $Parsed) {
+        try {
+            # todo: Trim sequences in \BioPHP\Transform->normalize()
+            $Trimmed = preg_replace('/\s+/', '', $Parsed['sequence']);
+            $Seqhash = $BioSeqhash->hash(
+                $Trimmed,
+                $_POST['seqhash_meta1'],
+                $_POST['seqhash_meta2'],
+                $_POST['seqhash_meta3']
+            );
+
+            $DB->query(
+                "
+            INSERT INTO `bioinformatics`
+              (`torrent_id`, `user_id`, `timestamp`,
+               `name`, `seqhash`)
+            VALUES (?, ?, NOW(), ?, ?)",
+                $TorrentID,
+                $LoggedUser['ID'],
+                $Parsed['name'],
+                $Seqhash
+            );
+        } catch (Exception $Err) {
+            $UploadForm = $Type;
+            require_once SERVER_ROOT.'/sections/upload/upload.php' ;
+            error($Err->getMessage(), $NoHTML = true);
+        }
+    }
+}
+
+
+/**
+ * Update tracker
+ */
 Tracker::update_tracker('add_torrent', [
   'id'          => $TorrentID,
   'info_hash'   => rawurlencode($InfoHash),

sections/user/community_stats.php

@@ -162,8 +162,8 @@ list($UniqueGroups) = $DB->next_record();
   if ($Override = check_paranoia_here('screenshotcount')) {
       $DB->query("
     SELECT COUNT(*)
-    FROM torrents_doi
-    WHERE UserID = '$UserID'");
+    FROM `literature`
+    WHERE user_id = '$UserID'");
       list($Screenshots) = $DB->next_record(); ?>
                 <li id="comm_screenshots">Screenshots added: <?=number_format($Screenshots)?>
                 </li>

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>