# BioMirror/EBI.pm

=head1 NAME

BioMirror::EBI -- BioMirror::Data packages for EMBL/EBI databanks

=cut


package BioMirror::SRSDatabanks;
@ISA = qw( BioMirror::Data );  
 
sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'DATABANKS',
		name => 'SRS Databanks',
		makeflags => $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		dosummary => 1, # add to summary table
   	source => { 	
   		home => 'EBI',
   		comment => 'List of active SRS databases around world',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/databanks/',
   		web => 'http://srs.ebi.ac.uk/',
   		## web => 'http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+pagelibinfo+-info+DATABANKS',
			},
			
		mirror_dir =>	'$zpath/srs-databanks/', 			
		expanded_dir =>	'$dpath/srs-databanks/',
		data => [ 'databanks.dat', ],
		@_ );
	return $self;
}

package BioMirror::Taxonomy_EBI; 
@ISA = qw( BioMirror::Data );  
 
sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'TAXONOMY',
		name => 'Taxonomy data from EBI',
		makeflags => $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		dosummary => 0, # add to summary table -- combine w/ NCBI taxonomy !
   	source => { 
   		home => 'EBI',
   		comment => 'Taxonomy data',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/',
			},
			
		mirror_dir =>	'$zpath/taxonomy/ebi/',  		
		expanded_dir =>	'$dpath/taxonomy/',
		data => [ 'taxonomy.dat', ],
		@_ );
	return $self;
}

package BioMirror::BiosoftCatalog; ## IUBio local db !	
## @ISA = qw( BioMirror::Data );  
## drop this; stale since 2000 ; jun03
 
sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'BIOCAT',
		name => 'Bio-Catalog',
		#skip#makeflags => $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		dosummary => 0, 
   	source => { 
   		comment => 'BioCatalog of Software from EBI',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/bio_catal/',
    	local_ignore => '([^Z]$|local$)',
		  recursive => 'false',
			},
			
		mirror_dir =>	'/bio/archive/biosoft-catalog/', 	## IUBio local !		
		expanded_dir =>	'/bio/biosoft-catalog/', ##? move to $dpath ?
		data => [ 'biocatal.txt', ],
		@_ );
	return $self;
}

package BioMirror::EMBL;
 @ISA = qw( BioMirror::Data ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'EMBL',
		name => 'EMBL',
		makeflags => 0, ##  no expansion or index ## $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		dosummary => 1, 
   	source => {
   		home => 'EBI',
   		comment => 'The EMBL Nucleotide Sequence Database',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/embl/release/',
   		web => 'http://www.ebi.ac.uk/embl/',
		  recursive => 'false',
			get_patt => '(\.dat\.gz$|^Release|README|\.doc$)',
    	exclude_patt => '(^gcg|^emvec|^Old)',
			},
			
		mirror_dir =>	'$zpath/embl/release/',
		expanded_dir =>	0, ##'$dpath/embl/',
		data => [],  ## no expansion
			
		@_ );
	return $self;
}

package BioMirror::EMBLNew;
 @ISA = qw( BioMirror::EMBL ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'EMBLNEW',
		name => 'EMBL Daily updates',
		makeflags => 0, ##  no expansion or index ## $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		dosummary => 0, 
   	source => {
   		comment => 'EMBL daily from EBI',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/embl/new/',
   		web => 'http://www.ebi.ac.uk/embl/',
			get_patt => '(^cum_\S+\.dat\.gz$|README)',
    	exclude_patt => '(^gcg|^list)',
		  recursive => 'false',
		  max_delete_files => '100%', # so old ones don't accumulate!
			},
			
		mirror_dir =>	'$zpath/embl/new/',
		expanded_dir =>	0, ##'$dpath/emblnew/',
		data => [],  ## no expansion
			
		@_ );
	return $self;
}

package BioMirror::TrEMBL;
 @ISA = qw( BioMirror::SwissProt ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'TREMBL',
		name => 'TrEMBL',
		makeflags => $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,
		mirror_dir =>	'$zpath/trembl/',
		expanded_dir =>	'$dpath/trembl/',

		dosummary => 1, 
   	source => {
   		home => 'EBI',
   		comment => 'A supplement to SWISS-PROT',
   		##url => 'ftp://expasy.hcuge.ch/databases/sp_tr_nrdb/', #? not responding
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/',
   		web => 'http://www.ebi.ac.uk/embl/',
    	get_patt => '(README|trembl.*\.dat\.Z$)', #? add sprot.dat.Z
     	local_ignore => '+Readme|update|log$',
     	exclude_patt => '+|fasta',
		  recursive => 'false',
			},

		data => [ 'trembl.dat', ],
		docs => [],
		@_ );
	return $self;
}


sub getRelease {
			# ???
	my $self= shift;
	my $rel= undef;
	my $df= BioMirror::replaceVars( $self->expanded_dir . ${$self->data}[0]);
	# my @df= $self->getDataPathnames(1);
	# my $df= $df[0] . $df[1];
	my $buf= $self->readChunk($df);

	#if ($buf =~ m/SWISS-PROT RELEASE ([0-9\.]+)/) {
	#	$rel= "$1";
	#	}
	return $rel;
}

#-------------

package BioMirror::TrEMBLNew;
 @ISA = qw( BioMirror::TrEMBL ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'TREMBLNEW',
		name => 'TrEMBL new data',
		makeflags => $BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,
		dosummary => 0, 

		sourceflags => $BioMirror::Data::kSuperSource,
		data => [ 'trembl_new.dat', ],
		@_ );
	return $self;
}


## add RELEASE 0.1 BETA OF InterPro
## yuck, its in xml 

package BioMirror::InterPro; 
@ISA = qw( BioMirror::Data );  
 
sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'INTERPRO',
		name => 'InterPro',
		makeflags => $BioMirror::Data::kFromArchive,
		  ## >> can't teach srs to do xml ? |$BioMirror::Data::kDoSrsIndex,

		dosummary => 1, 
   	source => { 
   		home => 'EBI',
   		comment => 'InterPro Protein databank',
   		url => 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/',
   		web => 'http://www.ebi.ac.uk/interpro',
			},
			
		mirror_dir =>	'$zpath/interpro/',  		
		expanded_dir =>	'$dpath/interpro/',
		data => [ '(i.*\.xml)', '(mat.*\.xml)',  '(\.dtd)', ],
		# jun01 - skip match*xml for now - SRS6.3 does handle it
		# doc => [ 'README', ],
		@_ );
	return $self;
}


1;