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lib/Bio/KBase/InvocationService/InvocationServiceImpl.pm  view on Meta::CPAN

    {
	die "Invalid path $dir";
    }

    my @dirs;
    my @files;
    my $dh;
    opendir($dh, $dir) or die "Cannot open directory: $!";
    while (my $file = readdir($dh)) {
	next if ($file =~ m/^\./);
	my($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks) = stat("$dir/$file");

	my $date= strftime("%b %d %G %H:%M:%S", localtime($mtime));

        if (-f "$dir/$file") {
	    push @files, { name => $file, full_path => "$fpath/$file", mod_date => $date, size => $size};
        } elsif (-d "$dir/$file") {
	    push @dirs, { name => $file, full_path => "$fpath/$file", mod_date => $date };
        }
    }

scripts/get_abundance_profile  view on Meta::CPAN

use warnings;
use JSON;
use Getopt::Long;
use LWP::UserAgent ;
use HTTP::Request::Common;

use Bio::KBase;

use Data::Dumper;

my $mgid   = "mgm4447970.3" ;
my $type   = "function";
my $format = 'plain' ;
my $source = 'Subsystems';
my $debug  = 0 ;

GetOptions (    
	    'id=s'     => \$mgid ,
	    'type=s'   => \$type , # "organism", "function", "feature"
	    'format=s' => \$format ,
	    'source=s' => \$source ,
	    'debug'    => \$debug  ,
    );



if ($mgid =~/^kb\|/){
    my $kb = Bio::KBase->new;
    my $idserver = $kb->id_server;

    my $return = $idserver->kbase_ids_to_external_ids( [ $mgid ]);
    $mgid = $return->{$mgid}->[1] ;
}


my $ua = LWP::UserAgent->new;
$ua->agent("KBASE/0.1 ");


# Create a request
my $base_url = "http://dev.metagenomics.anl.gov/api.cgi/" ;
#my $base_url = "http://dunkirk.mcs.anl.gov/~tharriso/mgrast/api.cgi/";
my $url      = $base_url . "abundance_profile/".$mgid."?format=".$format."&type=".$type."&source=".$source;

my $req = HTTP::Request->new(GET => "$url");
my $res = $ua->request($req);

if ($res->is_success){

  if ($res->header('Content-Type') eq "application/json") {
    
    my $json = JSON->new->allow_nonref;
    my $biom = $json->decode( $res->decoded_content );