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=head1 LICENSE

See the NOTICE file distributed with this work for additional information
regarding copyright ownership.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=cut

=head1 NAME

Bio::EnsEMBL::IdMapping::Archiver - create gene_archive and peptide_archive

=head1 SYNOPSIS

  my $archiver = Bio::EnsEMBL::IdMapping::Archiver->new(
    -LOGGER => $logger,
    -CONF   => $conf,
    -CACHE  => $cache
  );

  # create gene and peptide archive
  $archiver->create_archive($mapping_session_id);

  # dump existing archive tables to file
  my $num_entries =
    $archiver->dump_table_to_file( 'source', 'gene_archive',
    'gene_archive_existing.txt', 1 );

=head1 DESCRIPTION

This module creates the gene_archive and peptide_archive
tables. Data is written to a file as tab-delimited text for
loading into a MySQL database (this can be done manually, or using
StableIdmapper->upload_file_into_table()).

An archive entry for a given source gene is created if no target
gene exists, or if any of its transcripts or their translations
changed. Non-coding transcripts only have an entry in gene_archive (i.e.
without a corresponding peptide_archive entry).

=head1 METHODS

  create_archive
  dump_gene
  dump_tuple
  dump_nc_row
  mapping_session_id

=cut


package Bio::EnsEMBL::IdMapping::Archiver;
$Bio::EnsEMBL::IdMapping::Archiver::VERSION = '114.0.0';
use strict;
use warnings;
no warnings 'uninitialized';

use Bio::EnsEMBL::IdMapping::BaseObject;
our @ISA = qw(Bio::EnsEMBL::IdMapping::BaseObject);

use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
use Digest::MD5 qw(md5_hex);


# instance variables
my $pa_id;


=head2 create_archive

  Arg[1]      : Int $mapping_session_id - the mapping_session_id for this run
  Example     : $archiver->create_archive($stable_id_mapper->mapping_session_id);
  Description : Creates the gene_archive and peptide_archive tables and writes
                the data to a tab-delimited file. The decision as to what to
                archive is deferred to dump_gene(), see documentation there for
                details.
  Return type : none
  Exceptions  : Thrown on missing argument.
  Caller      : id_mapping.pl
  Status      : At Risk
              : under development

=cut

sub create_archive {
  my $self = shift;
  my $mapping_session_id = shift;

  # argument check
  unless ($mapping_session_id) {
    $self->logger->warning("No mapping_session_id set.");
  }