#!/usr/bin/env perl
############################################################
#
# $Id: supported-organisms-ucsc,v 1.4 2012/12/27 16:04:43 jvanheld Exp $
#
############################################################

## use strict;

=pod

=head1 NAME

suuported-organism-uscs

=head1 AUTHORS

=over

=item Jeremy Delerce

=item Jacques.van-Helden\@univ-amu.fr

=back

=head1 VERSION

$program_version

=head1 DESCRIPTION

Get the list of organisms available at the UCSC Genome browser
(http://genome.ucsc.edu/).

=head1 USAGE

supported-organims-uscs.pl [-o file] [-v #] [...]

Examples

Retrieve mammal genome disponible on UCSC.

 supported-organisms-ucsc -v 1

=cut

BEGIN {
  if ($0 =~ /([^(\/)]+)$/) {
    push (@INC, "$`lib/");
  }
}
require "RSA.lib";

#use Bio::Das; ## Required to access UCSC Genome Browser
use REST::Client;
use JSON;
#use Data::Dumper;

## Main package
package main;
{

  ################################################################
  ## Initialise parameters
  our $start_time = &RSAT::util::StartScript();
  our $program_version = do { my @r = (q$Revision: 1.4 $ =~ /\d+/g); sprintf "%d."."%02d" x $#r, @r };
  #    $program_version = "0.00";

#  our $taxon = "";
#  our $id_ok = "";
  our %outfile = ();
  our $verbose = 0;

  ## Get the list of organisms via the REST interface
  our $rest_server_url = "https://api.genome.ucsc.edu/list/ucscGenomes";
  
  ## Parameters for connecting the DAS server
#  our $das_server_url ="http://genome.cse.ucsc.edu/cgi-bin/das";

  ################################################################
  ## Read argument values
  &ReadArguments();

#   ################################################################
#   ## Define the URL fo the DAS server
# #  our $das_server_url = $das_server;
#   &RSAT::message::Info("DAS server", $das_server_url) if ($main::verbose >= 2);

#   ## Open DAS client
#   my $das = Bio::Das->new(30);  # timeout of 10 sec => not enough for UCSC, changed to 30 sec (MTC, 16 Feb 2015)
#   unless ($das) {
#     &RSAT::error::FatalError("Cannot establish connection to UCSC DAS server", $das_server_url);
#   }

  ################################################################
  ## Open output stream
  $out = &OpenOutputFile($outfile{output});

  ################################################################
  ## Print verbose
  &Verbose() if ($main::verbose >= 1);

  ################################################################
  ## REST request

  &RSAT::message::TimeWarn("Sending request to REST server", $rest_server_url) if ($main::verbose >= 3);

  our $client = REST::Client->new();
  $client->GET($rest_server_url);

  our $response = $client->responseContent();
  our $decoded = decode_json($response);

#  print Dumper($decoded);

  if ($main::verbose >= 1) {
      print $out "; REST URL        \t", $rest_server_url, "\n";
      print $out "; dataTime         \t", $decoded->{dataTime}, "\n";
      print $out "; dataTimeStamp    \t", $decoded->{dataTimeStamp}, "\n";
      print $out "; downloadTime     \t", $decoded->{downloadTime}, "\n";
      print $out "; downloadTimeStamp\t", $decoded->{downloadTimeStamp}, "\n";
  }
  
  print join("; ", keys(%$decoded)), "\n";
  our $genomes = $decoded->{"ucscGenomes"};
  our @ids = keys(%$genomes);

  for my $id (sort @ids) {
      my $scientific_name = $decoded->{"ucscGenomes"}->{$id}->{"scientificName"};
      print $out join("\t", $id, $scientific_name), "\n";
  }
  
  
  ## Send request to DAS server to obtain the list of supported organisms
  # &RSAT::message::TimeWarn("Sending request to DAS server", $das_server_url) if ($main::verbose >= 3);
  # my @response = $das->dsn('http://genome.cse.ucsc.edu/cgi-bin/das');


#  print("Response\n", @response);
  
#  &RSAT::message::Info("UCSC DAS response");
  
#   for my $url (@response) {
#     &RSAT::message::Info("\tURL\t\t", $url);
# #    &RSAT::message::Info("\tis_success\t", $url->is_success);
#     if ($url->is_success) {
#       my @dsns = $url->results;
#       foreach (@dsns) {
#         print $out $_->id,"\t",$_->description,"\n";
#       } 
#     } else {
# 	&RSAT::message::Warning("DAS request returned error");
# #	&RSAT::message::Info("Request DSN: ", $request->dsn,": ", $request->error);
#     }
#   }

  ################################################################
  ## Report execution time and close output stream
  my $exec_time = &RSAT::util::ReportExecutionTime($start_time); ## This has to be exectuted by all scripts
  print $out $exec_time if ($main::verbose >= 1); ## only report exec time if verbosity is specified
  close $out if ($outfile{output});

  exit(0);
}


################################################################
################### SUBROUTINE DEFINITION ######################
################################################################


################################################################
## Display full help message 
sub PrintHelp {
  system "pod2text -c $0";
  exit()
}

################################################################
## Display short help message
sub PrintOptions {
  &PrintHelp();
}

################################################################
## Read arguments 
sub ReadArguments {
  my $arg;
  my @arguments = @ARGV; ## create a copy to shift, because we need ARGV to report command line in &Verbose()
  while (scalar(@arguments) >= 1) {
    $arg = shift (@arguments);
    ## Verbosity

=pod

=head1 OPTIONS

=over 4

=item B<-v #>

Level of verbosity (detail in the warning messages during execution)

=cut
    if ($arg eq "-v") {
      if (&IsNatural($arguments[0])) {
	$main::verbose = shift(@arguments);
      } else {
	$main::verbose = 1;
      }

=pod

=item B<-h>

Display full help message

=cut
    } elsif ($arg eq "-h") {
      &PrintHelp();

=pod

=item B<-help>

Same as -h

=cut
    } elsif ($arg eq "-help") {
      &PrintOptions();

=pod

=item	B<-o outputfile>

The output file is in fasta format.

If no output file is specified, the standard output is used.  This
allows to use the command within a pipe.

=cut
    } elsif ($arg eq "-o") {
      $outfile{output} = shift(@arguments);

    } else {
      &FatalError(join("\t", "Invalid option", $arg));

    }
  }
}

################################################################
## Verbose message
sub Verbose {
  print $out "; supported-organisms-ucsc ";
  &PrintArguments($out);
  printf $out "; %-22s\t%s\n", "Program version", $program_version;
  if (%main::infile) {
    print $out "; Input files\n";
    while (my ($key,$value) = each %main::infile) {
      printf $out ";\t%-13s\t%s\n", $key, $value;
    }
  }
  if (%main::outfile) {
    print $out "; Output files\n";
    while (my ($key,$value) = each %main::outfile) {
      printf $out ";\t%-13s\t%s\n", $key, $value;
    }
  }
}