Add basic bioinformatics support

classes/config.template.php

@@ -1,4 +1,3 @@
-
 <?php
 declare(strict_types=1);
 
@@ -127,6 +126,7 @@ 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 +136,7 @@ ENV::setPub(
     'HELP',
     $ENV->convert($TechSupport)
 );
+*/
 
 
 /**
@@ -380,7 +381,8 @@ 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 +833,9 @@ $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 +976,23 @@ $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 +1348,11 @@ $CATS = [
         'Icon' => "$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 +1362,9 @@ $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 +1375,9 @@ $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 +1388,9 @@ $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 +1401,9 @@ $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 +1414,9 @@ $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 +1427,9 @@ $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 +1440,8 @@ $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 +1452,10 @@ $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 +1466,10 @@ $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 +1480,9 @@ $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 +1493,7 @@ $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 +1511,10 @@ 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/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",

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;
 
 

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
         $DB->query("
         SELECT
-          `ID`,
-          `UserID`,
-          `Time`,
-          `URI`
+          `id`,
+          `user_id`,
+          `timestamp`,
+          `resource`
         FROM
           `torrents_mirrors`
         WHERE
-          `GroupID` = '$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>