idf2chadoxml.pl

#!/usr/bin/perl

use strict;

my $root_dir;
BEGIN {
  $root_dir = $0;
  $root_dir =~ s/[^\/]*$//;
  $root_dir = "./" unless $root_dir =~ /\//;
  push @INC, $root_dir;
}
use Carp qw(croak carp);

use ModENCODE::ErrorHandler qw(log_error);
use ModENCODE::Config;
use ModENCODE::Cache;
use ModENCODE::Parser::IDF;
use ModENCODE::Validator::IDF_SDRF;
use ModENCODE::Validator::ModENCODE_Projects;
use ModENCODE::Validator::ModENCODE_Dates;
use ModENCODE::Validator::Wiki;
use ModENCODE::Validator::Attributes;
use ModENCODE::Validator::Data;
use ModENCODE::Validator::TermSources;
use ModENCODE::Chado::XMLWriter;

ModENCODE::ErrorHandler::set_logtype(ModENCODE::ErrorHandler::LOGGING_PREFIX_ON);
ModENCODE::Config::set_cfg($root_dir . 'validator.ini');
ModENCODE::Cache::init();


log_error "Validating submission...", "notice", ">";
# Get IDF file
my $idf = $ARGV[0];
{
  my ($path, $file) = ($idf =~ m/(.*?)([^\/]+$)/);
  $path = "." unless length($path);
  $path .= "/" unless $path =~ m/\/$/;
  chdir $path;
  $idf = $file;
}
log_error "Reading IDF and SDRF...", "notice", ">";

my $parser = new ModENCODE::Parser::IDF($idf);
my $result = $parser->parse();

if (!$result) {
  log_error "Failed.", "error", "<";
  exit;
}

log_error "Done.", "notice", "<";

my ($experiment, $protocols, $sdrfs, $termsources) = @$result;

log_error "Merging SDRF and IDF.", "notice", ">";
my $idf_validator = new ModENCODE::Validator::IDF_SDRF({
    'idf_experiment' => $experiment,
    'sdrf_experiment' => $sdrfs->[0],
    'protocols' => $protocols,
    'termsources' => $termsources,
  });
$experiment = $idf_validator->validate();
$idf_validator = undef;
$termsources = undef;
$sdrfs = undef;
$protocols = undef;
if (!$experiment) {
  log_error "Failed.", "error", "<";
  exit;
}
log_error "Done.", "notice", "<";

log_error "Validating presence of valid ModENCODE project/subproject names...", "notice", ">";
my $project_validator = new ModENCODE::Validator::ModENCODE_Projects({ 'experiment' => $experiment });
if (!$project_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}
$project_validator = undef;
log_error "Done.", "notice", "<";

log_error "Validating presence of public release and generation dates...", "notice", ">";
my $date_validator = new ModENCODE::Validator::ModENCODE_Dates({ 'experiment' => $experiment });
if (!$date_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}
$date_validator = undef;
log_error "Done.", "notice", "<";

log_error "Validating IDF and SDRF vs wiki...", "notice", ">";
my $wiki_validator = new ModENCODE::Validator::Wiki({ 'experiment' => $experiment });
if (!$wiki_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}
$wiki_validator = undef;
log_error "Done", "notice", "<";


log_error "Expanding attribute columns.", "notice", ">";
my $attribute_validator = new ModENCODE::Validator::Attributes({ 'experiment' => $experiment });
if (!$attribute_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}
$attribute_validator = undef;
log_error "Done.", "notice", "<";

log_error "Reading data files.", "notice", ">";
my $data_validator = new ModENCODE::Validator::Data({ 'experiment' => $experiment });
if (!$data_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}
$data_validator = undef;
log_error "Done.", "notice", "<";

log_error "Validating CVTerms and DBXrefs.", "notice", ">";
my $termsource_validator = new ModENCODE::Validator::TermSources({ 'experiment' => $experiment });
if (!$termsource_validator->validate()) {
  log_error "Failed.", "error", "<";
  exit;
}

log_error "Done.", "notice", "<";

log_error "Validated successfully!", "notice", "<";

log_error "Writing ChadoXML; this may take a while...", "notice", ">";
my $xmlwriter = new ModENCODE::Chado::XMLWriter();
if ($ARGV[1] && !$xmlwriter->set_output_file($ARGV[1])) {
  log_error "Failed to open " . $ARGV[1] . " for writing.", "error", "<";
  exit;
}
$xmlwriter->write_chadoxml($experiment);
log_error "Done. All tasks complete.", "notice", "<";

#print $experiment->to_string() . "\n";
ModENCODE::Cache::destroy();


1;