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#!/usr/bin/env perl
# PODNAME: import-itol.pl
# ABSTRACT: Upload trees and associate metadata files to iTOL
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use Smart::Comments '###';

use Archive::Zip qw(:ERROR_CODES :CONSTANTS);
use File::Basename;
use File::Find::Rule;
use HTTP::Request::Common;
use LWP::UserAgent;


my $upload_url = "https://itol.embl.de/batch_uploader.cgi";

# optionally setup tree id outfile
my $out;
if ($ARGV_tree_id_out) {
    open $out, '>', $ARGV_tree_id_out;
    say {$out} '# ' . join "\t", qw ( file id );
}

FILE:
for my $infile (@ARGV_infiles) {
    ### Processing: $infile

    # write ZIP archive file
    my $zip = Archive::Zip->new();
    my ($basename, $dir, $suffix) = fileparse($infile, qr{\.[^.]*}xms);
    my $zipfile = "$basename.zip";

    my $newname = "$basename.tree";     # iTOL wants a .tree suffix
    symlink($infile, $newname);         # TODO: improve this
    $zip->addFile($newname);

    $zip->addFile($_) for File::Find::Rule->file()
        ->maxdepth(1)->name("$basename\-*.txt")->in($dir);

    ### Storing ZIP file: $zipfile
    unless ( $zip->writeToFileNamed($zipfile) == AZ_OK ) {
        warn <<"EOT";
Warning: cannot ZIP archive file; skipping!
EOT
        next FILE;
    }

    # delete the symlink
    unlink($newname);                   # TODO: improve this

    # prepare the data
    my %data_for;
    $data_for{ 'zipFile'         } = [ $zipfile ];
    $data_for{ 'treeName'        } = $basename;
    $data_for{ 'APIkey'          } = $ARGV_api_key;
    $data_for{ 'projectName'     } = $ARGV_project;
    $data_for{ 'treeDescription' } = $ARGV_description if $ARGV_description;

    # submit the data
    my $ua = LWP::UserAgent->new();
    $ua->agent("iTOLbatchUploader4.0");
    my $request  = POST $upload_url,