Remove non-WiP packages

_packages/extension-parser/classes/config.php

@@ -1,104 +0,0 @@
-<?php
-
-# Line 222
-# Sequencing Formats
-#
-# https://www.ncbi.nlm.nih.gov/sra/docs/submitformats/
-$Containers = [
-  'BAM'        => ['bam'],
-  'CRAM'       => ['cram'],
-  'EMBL'       => ['embl'],
-  'FASTA'      => ['fa', 'fasta', 'fsa'],
-  'FASTA+QUAL' => ['qual'],
-  'CSFASTA'    => ['csfa', 'csfasta', 'csfsa'],
-  'FASTQ'      => ['fastq', 'fq', 'sanfastq'],
-  'GFF'        => ['gff', 'gff2', 'gff3'],
-  'GTF'        => ['gtf'],
-  'GenBank'    => ['gb', 'gbk', 'genbank'],
-  'HDF5'       => ['bash5', 'baxh5', 'fast5', 'hdf5'],
-  'PIR'        => ['pir'],
-  'QSeq'       => ['qseq'],
-  'SAM'        => ['sam'],
-  'SFF'        => ['sff'],
-  'SRF'        => ['srf'],
-  'SnapGene'   => ['dna', 'seq'],
-  'SwissProt'  => ['dat'],
-  'VCF'        => ['vcf'],
-  'Plain'      => ['csv', 'txt'],
-  'Other'      => [],
-];
-
-# Imaging Formats
-#
-# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948928/
-$ContainersGames = [
-  'Analyze'   => ['hdr', 'img'],
-  'Interfile' => ['h33'],
-  'DICOM'     => ['dcm', 'dicom'],
-  'NIfTI'     => ['nii', 'nifti'],
-  'MINC'      => ['minc', 'mnc'],
-  'JPEG'      => ['jfif', 'jpeg', 'jpg'],
-  'JPEG 2000' => ['j2k', 'jp2', 'jpf', 'jpm', 'jpx', 'mj2'],
-  'PNG'       => ['png'],
-  'TIFF'      => ['tif', 'tiff'],
-  'WebP'      => ['webp'],
-  'Other'     => [],
-];
-
-# Protein Formats
-# DON'T PARSE RAW FILES. TOO MANY COMPETING VENDORS
-#
-# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/
-$ContainersProt = [
-  'ABI/Sciex'      => ['t2d', 'wiff'],
-  'APML'           => ['apml'],
-  'ASF'            => ['asf'],
-  'Agilent/Bruker' => ['baf', 'd', 'fid', 'tdf', 'yep'],
-  'BlibBuild'      => ['blib'],
-  'Bruker/Varian'  => ['sms', 'xms'],
-  'Finnigan'       => ['dat', 'ms'],
-  'ION-TOF'        => ['ita', 'itm'],
-  'JCAMP-DX'       => ['jdx'],
-  'MGF'            => ['mgf'],
-  'MS2'            => ['ms2'],
-  'MSF'            => ['msf'],
-  'mzData'         => ['mzdata'],
-  'mzML'           => ['mzml'],
-  'mzXML'          => ['mzxml'],
-  'OMSSA'          => ['omssa', 'omx'],
-  'PEFF'           => ['peff'],
-  'pepXML'         => ['pepxml'],
-  'protXML'        => ['protxml'],
-  'Shimadzu'       => ['lcd', 'qgd', 'spc'],
-  'Skyline'        => ['sky', 'skyd'],
-  'TPP/SPC'        => ['dta'],
-  'Tandem'         => ['tandem'],
-  'TraML'          => ['traml'],
-  'ULVAC-PHI'      => ['tdc'],
-  'Plain'          => ['csv', 'txt'],
-  'Other'          => [],
-];
-
-# Extra Formats
-# DON'T PARSE IMG OR ISO FILES
-#
-# https://en.wikipedia.org/wiki/Disk_image#File_formats
-# https://en.wikipedia.org/wiki/OpenDocument
-# https://en.wikipedia.org/wiki/List_of_Microsoft_Office_filename_extensions
-# http://dcjtech.info/topic/python-file-extensions/
-$ContainersExtra = [
-  'Docker'           => ['dockerfile'],
-  'Hard Disk'        => ['fvd', 'dmg', 'esd', 'qcow', 'qcow2', 'qcow3', 'smi', 'swm', 'vdi', 'vhd', 'vhdx', 'vmdk', 'wim'],
-  'Optical Disc'     => ['bin', 'ccd', 'cso', 'cue', 'daa', 'isz', 'mdf', 'mds', 'mdx', 'nrg', 'uif'],
-  'Python'           => ['pxd', 'py', 'py3', 'pyc', 'pyd', 'pyde', 'pyi', 'pyo', 'pyp', 'pyt', 'pyw', 'pywz', 'pyx', 'pyz', 'rpy', 'xpy'],
-  'Jupyter Notebook' => ['ipynb'],
-  'Ontology'         => ['cgif', 'cl', 'clif', 'csv', 'htm', 'html', 'kif', 'obo', 'owl', 'rdf', 'rdfa', 'rdfs', 'rif', 'tsv', 'xcl', 'xht', 'xhtml', 'xml'],
-  'OpenDocument'     => ['odt', 'fodt', 'ods', 'fods', 'odp', 'fodp', 'odg', 'fodg', 'odf'],
-  'Word'             => ['doc', 'dot', 'wbk', 'docx', 'docm', 'dotx', 'dotm', 'docb'],
-  'Excel'            => ['xls', 'xlt', 'xlm', 'xlsx', 'xlsm', 'xltx', 'xltm', 'xlsb', 'xla', 'xlam', 'xll', 'xlw'],
-  'PowerPoint'       => ['ppt', 'pot', 'pps', 'pptx', 'pptm', 'potx', 'potm', 'ppam', 'ppsx', 'ppsm', 'sldx', 'sldm'],
-  'PDF'              => ['pdf', 'fdf', 'xfdf'],
-  'Plain'            => ['csv', 'txt'],
-  'Other'            => [],
-];
-# Line 321

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

@@ -1,132 +0,0 @@
-<?php
-
-class TorrentForm
-{
-    # Line 13
-    public $Containers = [];
-    public $ContainersGames = [];
-    public $ContainersProt = [];
-    public $ContainersExtra = [];
-    # Line 16
-
-    public function __construct($Torrent = false, $Error = false, $NewTorrent = true)
-    {
-        # Line 45
-        $this->Containers = $Containers;
-        $this->ContainersGames = $ContainersGames;
-        $this->ContainersProt = $ContainersProt;
-        $this->ContainersExtra = $ContainersExtra;
-        # Line 48
-?>
-
-<!-- Line 510 -->
-  <!-- Multiple container fields -->
-  <tr id="container_tr">
-    <td class="label">
-      Format
-      <strong class="important_text">*</strong>
-    </td>
-    <td>
-      <select id="container" name="container">
-        <option value="Autofill">Autofill</option>
-        <?php
-            foreach ($this->Containers as $Name => $Container) {
-                echo "\t\t\t\t\t\t<option value=\"$Name\"";
-                if ($Name === ($Torrent['Container'] ?? false)) {
-                    echo " selected";
-                }
-                echo ">$Name</option>\n";
-            } ?>
-      </select><br />
-      Data file format, or detect from file list
-    </td>
-  </tr>
-
-  <!-- 2 -->
-  <tr id="container_games_tr">
-    <td class="label">
-      Format
-      <strong class="important_text">*</strong>
-    </td>
-    <td>
-      <select id="container" name="container">
-        <option value="Autofill">Autofill</option>
-        <?php
-            foreach ($this->ContainersGames as $Name => $Container) {
-                echo "\t\t\t\t\t\t<option value=\"$Name\"";
-                if ($Name === ($Torrent['Container'] ?? false)) {
-                    echo " selected";
-                }
-                echo ">$Name</option>\n";
-            } ?>
-      </select><br />
-      Data file format, or detect from file list
-    </td>
-  </tr>
-
-  <!-- 3 -->
-  <tr id="container_prot_tr">
-    <td class="label">
-      Format
-      <strong class="important_text">*</strong>
-    </td>
-    <td>
-      <select id="container" name="container">
-        <option value="Autofill">Autofill</option>
-        <?php
-            foreach ($this->ContainersProt as $Name => $Container) {
-                echo "\t\t\t\t\t\t<option value=\"$Name\"";
-                if ($Name === ($Torrent['Container'] ?? false)) {
-                    echo " selected";
-                }
-                echo ">$Name</option>\n";
-            } ?>
-      </select><br />
-      Data file format, or detect from file list
-    </td>
-  </tr>
-
-  <!-- 4 -->
-  <tr id="container_extra_tr">
-    <td class="label">
-      Format
-      <strong class="important_text">*</strong>
-    </td>
-    <td>
-      <select id="container" name="container">
-        <option value="Autofill">Autofill</option>
-        <?php
-            foreach ($this->ContainersExtra as $Name => $Container) {
-                echo "\t\t\t\t\t\t<option value=\"$Name\"";
-                if ($Name === ($Torrent['Container'] ?? false)) {
-                    echo " selected";
-                }
-                echo ">$Name</option>\n";
-            } ?>
-      </select><br />
-      Data file format, or detect from file list
-    </td>
-  </tr>
-
-  <!-- Compression -->
-  <tr id="archive_tr">
-    <td class="label">
-      Archive
-      <strong class="important_text">*</strong>
-    </td>
-    <td>
-      <select id="archive" name="archive">
-        <option value="Autofill">Autofill</option>
-        <?php
-            foreach ($this->Archives as $Name => $Archive) {
-                echo "\t\t\t\t\t\t<option value=\"$Name\"";
-                if ($Name === ($Torrent['Archive'] ?? false)) {
-                    echo " selected";
-                }
-                echo ">$Name</option>\n";
-            } ?>
-      </select><br />
-      Compression algorithm, or detect from file list
-    </td>
-  </tr>
-<!-- Line 618 -->

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

@@ -1,66 +0,0 @@
-<?php
-
-class Validate
-{
-    # Line 171
-    /**
-     * Extension Parser
-     *
-     * Takes an associative array of file types and extension, e.g.,
-     * $Archives = [
-     *   '7z'     => ['7z'],
-     *   'bzip2'  => ['bz2', 'bzip2'],
-     *   'gzip'   => ['gz', 'gzip', 'tgz', 'tpz'],
-     *   ...
-     * ];
-     *
-     * Then it finds all the extensions in a torrent file list,
-     * organizes them by file size, and returns the heaviest match.
-     *
-     * That way, you can have, e.g., 5 GiB FASTQ sequence data in one file,
-     * and 100 other small files, and get the format of the actual data.
-     *
-     * todo: Incorporate into $this->ValidateForm (remove if statements first)
-     */
-    public function ParseExtensions($FileList, $Category, $FileTypes)
-    {
-        # Sort $Tor->file_list() output by size
-        $UnNested = array_values($FileList[1]);
-        $Sorted = (usort($UnNested, function ($a, $b) {
-            return $b <=> $a;
-        })) ? $UnNested : null;  # Ternary wrap because ↑ returns true
-        
-        # Harvest the wheat
-        # todo: Entries seem duplicated here
-        $Heaviest = array_slice($Sorted, 0, 20);
-        $Matches = [];
-
-        foreach ($Heaviest as $Heaviest) {
-            # Collect the last 2 period-separated tokens
-            $Extensions = array_slice(explode('.', strtolower($Heaviest[1])), -2, 2);
-            $Matches = array_merge($Extensions);
-
-            # Distill the file format
-            $FileTypes = $FileTypes[$Category];
-            $FileTypeNames = array_keys($FileTypes);
-
-            # todo: Find the smallest possible number of iterations
-            # todo: Reduce nesting by one level
-            foreach ($Matches as $Match) {
-                $Match = strtolower($Match);
-        
-                foreach ($FileTypeNames as $FileTypeName) {
-                    $SearchMe = [ $FileTypeName, $FileTypes[$FileTypeName] ];
-        
-                    if (in_array($Match, $SearchMe[1])) {
-                        return $SearchMe[0];
-                        break;
-                    } else {
-                        return 'Other';
-                    break;
-                    }
-                }
-            }
-        }
-    }
-    # Line 230

_packages/extension-parser/readme.md

@@ -1,40 +0,0 @@
-## Detect and autofill file types by extension
-
-One of the challenges of tracking biology data is the overwhelming number of file formats.
-If a user leaves the container or archive dropdown blank, this tool:
-  * Adds the file sizes of each extension
-  * Sorts the torrent file list by size
-  * Returns the first matching extension key
-
-## In this repo
-Please find all the snippets you need to implement a similar feature on your own tracker.
-See `classes/config.php` for an idea of how the each format is associated with an array of file extensions.
-I'll reproduce an example below so you can see how powerful a general extension parser can be.
-
-```php
-$ContainersExtra = [
-  'Docker'           => ['dockerfile'],
-  'Hard Disk'        => ['fvd', 'dmg', 'esd', 'qcow', 'qcow2', 'qcow3', 'smi', 'swm', 'vdi', 'vhd', 'vhdx', 'vmdk', 'wim'],
-  'Optical Disc'     => ['bin', 'ccd', 'cso', 'cue', 'daa', 'isz', 'mdf', 'mds', 'mdx', 'nrg', 'uif'],
-  'Python'           => ['pxd', 'py', 'py3', 'pyc', 'pyd', 'pyde', 'pyi', 'pyo', 'pyp', 'pyt', 'pyw', 'pywz', 'pyx', 'pyz', 'rpy', 'xpy'],
-  'Jupyter Notebook' => ['ipynb'],
-  'Ontology'         => ['cgif', 'cl', 'clif', 'csv', 'htm', 'html', 'kif', 'obo', 'owl', 'rdf', 'rdfa', 'rdfs', 'rif', 'tsv', 'xcl', 'xht', 'xhtml', 'xml'],
-  'OpenDocument'     => ['odt', 'fodt', 'ods', 'fods', 'odp', 'fodp', 'odg', 'fodg', 'odf'],
-  'Word'             => ['doc', 'dot', 'wbk', 'docx', 'docm', 'dotx', 'dotm', 'docb'],
-  'Excel'            => ['xls', 'xlt', 'xlm', 'xlsx', 'xlsm', 'xltx', 'xltm', 'xlsb', 'xla', 'xlam', 'xll', 'xlw'],
-  'PowerPoint'       => ['ppt', 'pot', 'pps', 'pptx', 'pptm', 'potx', 'potm', 'ppam', 'ppsx', 'ppsm', 'sldx', 'sldm'],
-  'PDF'              => ['pdf', 'fdf', 'xfdf'],
-  'Plain'            => ['csv', 'txt'],
-  'Other'            => [],
-];
-```
-
-## Caveats and todos
-Test thoroughly before implementing to ensure the behavior is what you expect!
-You don't want to ruin the database with unextected "Autofill" formats.
-
-For this reason, extension parsing is disabled on the torrent edit handler for now.
-The FileList stored in the database, available to the edit form, is a bencoded string instead of a nested array.
-$Validate->ParseExtensions currently only works with the $Tor->FileList object before its bencoded.
-
-That's all for now.

_packages/extension-parser/sections/torrents/edit.php

@@ -1,3 +0,0 @@
-<?php
-
-# todo

_packages/extension-parser/sections/torrents/takeedit.php

@@ -1,23 +0,0 @@
-<?php
-
-# Line 58
-$Properties['Container'] = (isset($_POST['container']) && $_POST['container'] !== '---') ? $_POST['container'] : 'Other';
-$Properties['Archive'] = (isset($_POST['archive']) && $_POST['archive'] !== '---') ? $_POST['archive'] : 'None';
-# Line 59
-
-# Line 294
-//******************************************************************************//
-//--------------- Autofill format and archive ----------------------------------//
-
-# Load FileList in lieu of $Tor object
-# todo: Format the output for  $Validate->ParseExtensions()
-#var_dump($T['FileList']);
-
-# Disable the extension parser for edits
-# todo: Make this work with $T['FileList']
-if ($T['Container'] === 'Autofill'
-|| $T['Archive'] === 'Autofill') {
-    $Err = "Extension parsing is only possible for new uploads";
-    error($Err);
-}
-# Line 307

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

@@ -1,59 +0,0 @@
-<?php
-
-# Line 44
-# todo: Associate containers with categories beforehand
-# It may have to happen structurally in config.php, e.g.,
-# $Categories = [
-#   'GazelleName' => [$Name, $Icon, $Description, $Containers],
-#    ...
-#  ];
-$Properties['FileTypes'] = [
-    'DNA'      => $Containers,
-    'RNA'      => $Containers,
-    'Proteins' => $ContainersProt,
-    'Imaging'  => $ContainersGames,
-    'Extras'   => $ContainersExtra
-];
-$Properties['ArchiveTypes'] = [
-    'DNA'      => $Archives,
-    'RNA'      => $Archives,
-    'Proteins' => $Archives,
-    'Imaging'  => $Archives,
-    'Extras'   => $Archives
-];
-# Line 63
-
-# Line 427
-//******************************************************************************//
-//--------------- Autofill format and archive ----------------------------------//
-
-if ($T['Container'] === 'Autofill') {
-    # torrents.Container
-    $T['Container'] = $Validate->ParseExtensions(
-
-        # $FileList
-        $Tor->file_list(),
-
-        # $Category
-        $T['CategoryName'],
-
-        # $FileTypes
-        $T['FileTypes'],
-    );
-}
-
-if ($T['Archive'] === 'Autofill') {
-    # torrents.Archive
-    $T['Archive'] = $Validate->ParseExtensions(
-
-        # $FileList
-        $Tor->file_list(),
-
-        # $Category
-        $T['CategoryName'],
-
-        # $FileTypes
-        $T['ArchiveTypes'],
-    );
-}
-# Line 458

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

@@ -1,83 +0,0 @@
-// Line 11
-function Categories() {
-    let def = [
-      'javdb', // Accession Number
-      'audio', // Version
-      'title', // Torrent Title
-      'title_rj', // Organism
-      'title_jp', // Strain/Variety
-      'idols', // Authors(s)
-      'studio', // Department/Lab
-      'series', // Location
-      'year', // Year
-      'codec', // License
-      // Platform changes below
-      'resolution', // Assembly Level
-      // Format changes below
-      'archive', // Archive
-      'tags', // Tags
-      'cover', // Picture
-      'mirrors', // Mirrors
-      'screenshots', // Publications
-      'group_desc', // Torrent Group Description
-      'release_desc', // Torrent Description
-      'censored', // Aligned/Annotated
-      'anon', // Upload Anonymously
-    ]
-  
-    let cats = [
-      { // DNA
-        'media': {}, // Platform
-        'container': {}, // Format
-      },
-      { // RNA
-        'media': {}, // Platform
-        'container': {}, // Format
-      },
-      { // Proteins
-        'media': {}, // Platform
-        'container_prot': {}, // Format
-      },
-      { // Imaging
-        'media_manga': {}, // Platform
-        'container_games': {}, // Format
-      },
-      { // Extras
-        'media': {}, // Platform
-        'container_extra': {}, // Format
-      }
-    ]
-  
-    let active = {}
-    for (let field of def) active[field] = {}
-    let category = 0
-    if ($('input[name="type"]').raw()) category = $('input[name="type"]').raw().value
-    if ($('#categories').raw()) category = $('#categories').raw().value
-    active = Object.assign(active, cats[category])
-  
-    let hide = el => {
-      Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = true)
-      $(el).ghide()
-    }
-  
-    let show = el => {
-      Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = false)
-      $(el).gshow()
-    }
-  
-    let trs = $('#dynamic_form tr')
-    for (let tr of trs) {
-      let field = tr.id.slice(0, -3)
-      if (active[field]) {
-        if (active[field].name) {
-          tr.children[0].innerHTML = active[field].name
-        }
-        let notes = $(`#${tr.id} p.notes`).raw()
-        if (notes) notes.innerHTML = active[field].notes || ''
-        show(tr)
-      } else {
-        hide(tr)
-      }
-    }
-  }
-// Line 91

_packages/formatting-bugs

@@ -1 +0,0 @@
-Subproject commit 6139ce97dcb80d59e2e910345c5a72259a86e85b

_packages/tracker-tiers

@@ -1 +0,0 @@
-Subproject commit 8461f7a8d59abcddfbfd7611198427423a682829