File Coverage

blib/lib/PomBase/Chobo/ParseOBO.pm

Criterion	Covered	Total	%
statement	116	137	84.6
branch	55	70	78.5
condition	14	20	70.0
subroutine	5	7	71.4
pod	0	3	0.0
total	190	237	80.1

package PomBase::Chobo::ParseOBO;

=head1 NAME

PomBase::Chobo::ParseOBO - Parse the bits of an OBO file needed for
                           loading Chado

=head1 SYNOPSIS

=head1 AUTHOR

Kim Rutherford C<<  >>

=head1 BUGS

Please report any bugs or feature requests to C.

=head1 SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc PomBase::Chobo::ParseOBO

=over 4

=back

=head1 COPYRIGHT & LICENSE

Copyright 2012 Kim Rutherford, all rights reserved.

This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.

=head1 FUNCTIONS

=cut

our $VERSION = '0.041'; # VERSION

use Mouse;
use FileHandle;

use PomBase::Chobo::OntologyData;

sub die_line
{
  my $filename = shift;
  my $linenum = shift;
  my $message = shift;

  die "$filename:$linenum:$message\n";
}

sub _finish_stanza
{
  my $filename = shift;
  my $current = shift;
  my $terms_ref = shift;
  my $metadata_ref = shift;

  if ($current->{is_obsolete} && $current->{is_relationshiptype}) {
    return;
  }

  if (!defined $current->{name}) {
    warn "term without a name tag ignored: ", $current->{id}, "\n";
    return;
  }

  if (!defined $current->{id}) {
    die_line $filename,  $current->{line}, "stanza has no id\n";
    return;
  }

  if ($current->{id} !~ /:/) {
    # try to find a sensible ID if the ID looks like a name ("id: output_of")
    if ($current->{xref}) {
      for my $xref (@{$current->{xref}}) {
        if ($xref =~ /^RO:/) {
          $current->{id} = $xref;
          goto ID_FIXED
        }
      }

      for my $xref (@{$current->{xref}}) {
        if ($xref =~ /^BFO:/) {
          $current->{id} = $xref;
          goto ID_FIXED
        }
      }
    }
  }

  ID_FIXED:
  if ($current->{is_obsolete}) {
    delete $current->{alt_id};
  }

  $current->{metadata} = $metadata_ref;
  $current->{source_file} = $filename;
  $current->{relationship} //= [];

  my $namespace_from_metadata = 0;

  if (!defined $current->{namespace}) {
    $current->{namespace} =
      $metadata_ref->{'default-namespace'} //
      $metadata_ref->{'ontology'} //
      $current->{source_file} . '::' . $current->{id} =~ s/:.*//r;

    if ($current->{namespace} eq 'ro') {
      $current->{namespace} = 'relations';
    }

    $namespace_from_metadata = 1;
  }

  if ($current->{is_a}) {
    map {
      push @{$current->{relationship}},
        {
          'relationship_name' => 'is_a',
          'other_term' => $_,
        };
    } @{$current->{is_a}};

    delete $current->{is_a};
  }

  if ($current->{synonym}) {
    my %seen_synonyms = ();

    $current->{synonym} = [
      map {

        my $seen_synonym = $seen_synonyms{$_->{synonym}};
        if ($seen_synonym && lc $seen_synonym->{scope} eq 'exact') {
          # keep it
        } else {
          $seen_synonyms{$_->{synonym}} = $_;
        }
      } @{$current->{synonym}}
    ];

    $current->{synonym} = [sort { $a->{synonym} cmp $b->{synonym} } values %seen_synonyms];
  }

  my $options = { namespace_from_metadata => $namespace_from_metadata };

  my $new_term = PomBase::Chobo::OntologyTerm->make_object($current, $options);

  push @$terms_ref, $new_term;
}

sub fatal
{
  my $message = shift;

  die "fatal: $message\n";
}

my %interesting_metadata = (
  'default-namespace' => 1,
  'ontology' => 1,
  'date' => 1,
  'data-version' => 1,
);

sub parse
{
  my $self = shift;
  my %args = @_;

  my $filename = $args{filename};
  if (!defined $filename) {
    die 'no filename passed to parse()';
  }

  my $ontology_data = $args{ontology_data};
  if (!defined $ontology_data) {
    die 'no ontology_data passed to parse()';
  }

  my %metadata = ();
  my @terms = ();

  my $current = undef;
  my @synonyms = ();

  my %meta = ();

  open my $fh, '<:utf8', $filename or die "can't open $filename: $!";

  my $line_number = 0;;

  while (defined (my $line = <$fh>)) {
    $line_number++;
    chomp $line;
    $line =~ s/![^"\n]*$//;
    $line =~ s/\s+$//;
    $line =~ s/^\s+//;

    next if length $line == 0;

    if ($line =~ /^\[(.*)\]$/) {
      my $stanza_type = $1;

      if (defined $current) {
        _finish_stanza($filename, $current, \@terms, \%metadata);
      }

      my $is_relationshiptype = 0;

      if ($stanza_type eq 'Typedef') {
        $is_relationshiptype = 1;
      } else {
        if ($stanza_type ne 'Term') {
          die "unknown stanza type '[$stanza_type]'\n";
        }
      }
      $current = {
        is_relationshiptype => $is_relationshiptype,
        source_file_line_number => $line_number,
      };
    } else {
      if ($current) {
        my @bits = split /: /, $line, 2;
        if (@bits == 2) {
          my $field_name = $bits[0];
          my $field_value = $bits[1];

          # ignored for now
          my $modifier_string;

          if ($field_value =~ /\}$/) {
            $field_value =~ s/(.*)\{(.*)\}$/$1/;
            $modifier_string = $2;
            $field_value =~ s/\s+$//;
          }

          my $field_conf = $PomBase::Chobo::OntologyConf::field_conf{$field_name};

          if (defined $field_conf) {
            if (defined $field_conf->{process}) {
              eval {
                $field_value = $field_conf->{process}->($field_value);
              };
              if ($@) {
                warn qq(warning "$@" at $filename line $.\n);
              }
            }
            if (defined $field_value) {
              if (defined $field_conf->{type} &&
                  ($field_conf->{type} eq 'SINGLE' || $field_conf->{type} eq 'SINGLE_HASH')) {
                $current->{$field_name} = $field_value;
              } else {
                push @{$current->{$field_name}}, $field_value;
              }
            }
          }
        } else {
          die "can't parse line - no colon: $line\n";
        }
      } else {
        # we're parsing metadata
        if ($line =~ /^(.+?):\s*(.*)/) {
          my ($key, $value) = ($1, $2);

          if ($interesting_metadata{$key}) {
            if (defined $metadata{$key}) {
              warn qq(metadata key "$key" occurs more than once in header\n);
            } else {
              $metadata{$key} = $value;
            }
          }
        } else {
          fatal "can't parse header line: $line";
        }
      }
    }
  }

  if (defined $current) {
    _finish_stanza($filename, $current, \@terms, \%metadata);
  }

  close $fh or die "can't close $filename: $!";

  eval {
    $ontology_data->add(metadata => \%metadata,
                        terms => \@terms);
  };
  if ($@) {
    die "failed while reading $filename: $@\n";
  }
}

1;