=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

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

package XrefParser::VegaOfficialNameParser;

use strict;
use warnings;
use Carp;
use DBI;
use Bio::EnsEMBL::Registry;
use base qw( XrefParser::BaseParser );
my $reg = "Bio::EnsEMBL::Registry";

sub run_script {

  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $file         = $ref_arg->{file};
  my $verbose      = $ref_arg->{verbose};

  if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
    croak "Need to pass source_id, species_id and file as pairs";
  }
  $verbose |=0;

  my ($type, $my_args) = split(/:/,$file);

  my ($host, $source_name);
  if($my_args =~ /host[=][>](\S+?)[,]/){
    $host = $1;
  }
  if ($my_args =~ /source[=][>](\S+?)[,]/) {
    $source_name = $1;
  }

  my %id2name = $self->species_id2name;
  my $species_name = $id2name{$species_id}[0];

  my $prepend = 1;
  if($species_name eq "mus_musculus" || $species_name eq 'homo_sapiens'){
    $prepend = 0;
  }

  my $user = 'ensro';
  if($my_args =~ /user[=][>](\S+?)[,]/){
    $user = $1;
  }

  my $vuser = 'ensro';
  my $vhost;
  my $vport = 3306;
  my $vdbname;
  my $vpass;

  if($my_args =~ /vhost[=][>](\S+?)[,]/){
    $vhost = $1;
  }
  if($my_args =~ /vuser[=][>](\S+?)[,]/){
    $vuser = $1;
  }
  if($my_args =~ /vport[=][>](\S+?)[,]/){
    $vport =  $1;
  }
  if($my_args =~ /vdbname[=][>](\S+?)[,]/){
    $vdbname = $1;
  }
  if($my_args =~ /vpass[=][>](\S+?)[,]/){
    $vpass = $1;
  }

  my $cuser = 'ensro';
  my $chost;
  my $cport = 3306;
  my $cdbname;
  my $cpass;

  if($my_args =~ /chost[=][>](\S+?)[,]/){
    $chost = $1;
  }
  if($my_args =~ /cuser[=][>](\S+?)[,]/){
    $cuser = $1;
  }
  if($my_args =~ /cport[=][>](\S+?)[,]/){
    $cport =  $1;
  }
  if($my_args =~ /cdbname[=][>](\S+?)[,]/){
    $cdbname = $1;
  }
  if($my_args =~ /cpass[=][>](\S+?)[,]/){
    $cpass = $1;
  }

  my $vega_dbc;
  my $core_dbc;

  if(defined($vdbname)){
    print "Using $vhost $vdbname for Vega and $cdbname for Core\n";
    my $vega_db =  XrefParser::Database->new({ host   => $vhost,
					       port   => $vport,
					       user   => $vuser,
					       dbname => $vdbname,
					       pass   => $vpass});

    $vega_dbc = $vega_db->dbi();
    if(!defined($vega_dbc)){
      print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
      return 1;
    }
  } else{
    $reg->load_registry_from_db(
                                -host => $host,
                                -port => 4519,
                                -user => $user);

    $vega_dbc = $reg->get_adaptor($species_name,"vega","slice");
    if(!defined($vega_dbc)){
      print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n";
      return 1;
    }
    $vega_dbc = $vega_dbc->dbc;
 }
 if (defined $cdbname) {
    my $core_db =  XrefParser::Database->new({ host   => $chost,
                                               port   => $cport,
                                               user   => $cuser,
                                               dbname => $cdbname,
                                               pass   => $cpass});

    $core_dbc = $core_db->dbi();
    if(!defined($core_dbc)){
      print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
      return 1;
    }

  } else {
    $reg->load_registry_from_db(
                                -host => $host,
                                -port => 4519,
                                -user => $user);

    $core_dbc = $reg->get_adaptor($species_name,"core","slice");
    if(!defined($core_dbc)){
      print "Could not connect to $species_name core database using load_registry_from_db $host $user\n";
      return 1;
    }
    $core_dbc= $core_dbc->dbc;
  }



  $source_id = $self->get_source_id_for_source_name($source_name,"vega");


  my $sql =(<<SQL);
SELECT t.stable_id, x.display_label 
  FROM analysis a, xref x, object_xref ox , transcript t, external_db e
   WHERE a.analysis_id = t.analysis_id and 
         e.external_db_id = x.external_db_id and 
         x.xref_id = ox.xref_id and 
         t.transcript_id = ox.ensembl_id and
         a.logic_name like "%havana%" and 
         e.db_name like ?
SQL

  my $ext_sql =(<<EXT);
SELECT t.stable_id, x.dbprimary_acc 
  FROM xref x, object_xref ox , transcript t, gene g, external_db e 
    WHERE t.gene_id = g.gene_id and 
          g.gene_id = ox.ensembl_id and 
          e.external_db_id = x.external_db_id and 
          x.xref_id = ox.xref_id and 
          ox.ensembl_object_type = "Gene" and 
          e.db_name like '$source_name'
EXT

  my %vega_to_ext;
  my %ext_to_core;

  my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";


  foreach my $external_db (qw(Vega_transcript shares_CDS_with_OTTT shares_CDS_and_UTR_with_OTTT OTTT)){
    $sth->execute($external_db) or croak( $core_dbc->errstr());
    while ( my @row = $sth->fetchrow_array() ) {
      $ext_to_core{$row[1]} = $row[0];
    }
  }

  print "We have ".scalar(%ext_to_core)." vega to external source entries\n " if($verbose);

  $sth = $vega_dbc->prepare($ext_sql) || die "could not prepare vega sql: $ext_sql";
  $sth->execute() or croak( $vega_dbc->errstr() );

  while ( my @row = $sth->fetchrow_array() ) {
    $vega_to_ext{$row[0]} = $row[1];
  }
  $sth->finish;
  print "We have ".scalar(%vega_to_ext)." vega to external source entries\n" if($verbose);


  my $line_count = 0;
  my $xref_count = 0;

  # becouse the direct mapping have no descriptions etc
  # we have to steal these fromt he previous external source parser.
  # This is why the order states this is after the other one.

  my %label;
  my %version;
  my %description;

  my $dbi = $self->dbi();  


  my $syn_sql = "insert ignore into synonym (xref_id, synonym) values (?, ?)";
  my $add_syn_sth = $dbi->prepare($syn_sql);    
  
  my $syn_hash = $self->get_ext_synonyms($source_name);

  $sql = 'select source_id, priority_description from source where name like "' . $source_name . '"';
  $sth = $dbi->prepare($sql);
  
  $sth->execute();

  my ($ext_source_id, $desc);
  $sth->bind_columns(\$ext_source_id, \$desc);
  my @arr;
  while($sth->fetch()){
    push @arr, $ext_source_id;
  }
  $sth->finish;
  
  $sql = "select accession, label, version,  description from xref where source_id in (".join(", ",@arr).")";
#  print "$sql\n";;
  $sth = $dbi->prepare($sql);
  $sth->execute();
  my ($acc, $lab, $ver);
  my $ext_loaded_count = 0;
  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
  while ($sth->fetch()) {
    $label{$acc} = $lab;
    $version{$acc} = $ver;
    $description{$acc} = $desc if(defined($desc));
    $ext_loaded_count++;
  }
  $sth->finish;
  if($ext_loaded_count == 0){
    warn "No point continuing, no external references there\n";
    return 0;
  }

  my $ignore_count = 0;
  my $ignore_examples ="";
  my %acc;

  my $at_least_1_xref_loaded = 0;

  foreach my $key ( keys %vega_to_ext){
    if(defined($ext_to_core{$key} )){
      
      my $ext = $vega_to_ext{$key};
      if($prepend){
	my $regex = $source_name . ':';
	$ext =~ s/$regex//;
      }
      my $stable_id = $ext_to_core{$key};

      if(!defined($label{$ext})){
	$ignore_count++;
	if($ignore_count < 10){
	  $ignore_examples .= " ".$ext." (". $vega_to_ext{$key} ." )";
	}
	next;
      }

      
      my $version ="";
      $line_count++;
      if(!defined($acc{$ext})){
	my $xref_id = $self->add_xref({ acc        => $ext,
					version    => $version{$ext} ,
					label      => $label{$ext}||$ext ,
					desc       => $description{$ext},
					source_id  => $source_id,
					species_id => $species_id,
					info_type  => "DIRECT"} );

	$acc{$ext} = $xref_id;
	$xref_count++;
	if ((defined($xref_id)) and ($at_least_1_xref_loaded == 0)){
	   $at_least_1_xref_loaded = 1;
	}
      }
	
	
      $self->add_direct_xref($acc{$ext}, $stable_id, "transcript", "");

      if(defined($syn_hash->{$ext})){
	foreach my $syn (@{$syn_hash->{$ext}}){
	  $add_syn_sth->execute($acc{$ext}, $syn);
	}
      }
      
    }
  }
  $add_syn_sth->finish;

  print "Parsed $line_count $source_name identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n" if($verbose);
  if($ignore_count){
    print $ignore_count." ignored due to numbers no identifiers being no longer valid :- $ignore_examples\n" if($verbose);
  }
  
  if ($at_least_1_xref_loaded == 0) {    
      print "None of the external references were loaded to the core database.\n";
      return 1;
  }
  return 0;
}

1;