From 4283b9b5eb537f82579403ec071e3dd091b8ea1d Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 20 Apr 2011 13:03:28 +0000
Subject: [PATCH] *** empty log message ***
---
misc-scripts/link_out/generate_LinkOut.pl | 226 ++++++++++++++++++++++
misc-scripts/link_out/linkOut_config.txt | 2 +
2 files changed, 228 insertions(+)
create mode 100644 misc-scripts/link_out/generate_LinkOut.pl
create mode 100644 misc-scripts/link_out/linkOut_config.txt
diff --git a/misc-scripts/link_out/generate_LinkOut.pl b/misc-scripts/link_out/generate_LinkOut.pl
new file mode 100644
index 0000000000..f2a5707c1b
--- /dev/null
+++ b/misc-scripts/link_out/generate_LinkOut.pl
@@ -0,0 +1,226 @@
+# Generate LinkOut resource file for NCBI website.
+# Author: Monika Komorowska
+# Date : 06.04.2011
+
+# Upload generated files:
+# http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Transferring_Files_via_FTP
+
+
+use strict;
+use DBI;
+use Getopt::Long;
+
+sub new_file;
+
+my ( $dbpattern, $out_file, $config_file );
+
+GetOptions( "dbpattern|pattern=s", \$dbpattern,
+ "out_file=s", \$out_file,
+ "config_file=s", \$config_file,
+ );
+
+if( !$dbpattern ) {
+ usage();
+}
+
+if (!$config_file) {
+ $config_file = "linkOut_config.txt";
+}
+
+open( CFH, "<$config_file" ) or die("Can't open $config_file\n");
+my @hosts;
+while (my $line = <CFH>) {
+ push( @hosts, $line);
+}
+close CFH;
+
+if( !$out_file ) {
+ $out_file = "resources";
+}
+
+my $file_size;
+my $number_of_files = 1;
+
+my $header = <<HEADER;
+<?xml version="1.0"?>
+<!DOCTYPE LinkSet PUBLIC "-//NLM//DTD LinkOut 1.0//EN"
+"http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/LinkOut.dtd"
+[<!ENTITY base.url "http://www.ensembl.org/id/">]>
+
+<LinkSet>
+HEADER
+
+my $header_size;
+{
+ use bytes;
+ $header_size = length($header);
+}
+
+new_file();
+my $link_no = 0;
+
+foreach my $host_line (@hosts) {
+ $host_line =~ /([^\s]+)\s+([^\s]+)\s*(\d*)/;
+ my $host = $1;
+ my $user = $2;
+ my $port = $3;
+
+ my $dsn = "DBI:mysql:host=$host";
+ if( $port =~ /\d+/) {
+ $dsn .= ";port=$port";
+ }
+ my $db = DBI->connect( $dsn, $user);
+ if (!defined $db) {
+ my $message = "Can't connect to host: $host, port: ";
+ if($port =~ /\d+/) {
+ $message .= $port;
+ } else {
+ $message .= 'default';
+ }
+ $message .= ", user: $user\n";
+ print STDOUT $message;
+ next;
+ }
+
+ my @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
+
+ for my $dbname ( @dbnames ) {
+ if( $dbpattern ) {
+ if( $dbname !~ /$dbpattern/ ) {
+ next;
+ }
+ }
+
+ $db->do( "use $dbname" );
+ #get nucleotide data
+ my ($entrez_db, $ref_seq_accession,$ensembl_stable_id);
+ my $current_file_no = $number_of_files;
+ $entrez_db = "Nucleotide";
+
+ my $sth = $db->prepare("SELECT dbprimary_acc, stable_id FROM object_xref o INNER JOIN xref x on o.xref_id = x.xref_id INNER JOIN external_db e on e.external_db_id =x.external_db_id INNER JOIN transcript_stable_id on ensembl_id = transcript_id WHERE db_name in ('RefSeq_dna', 'RefSeq_dna_predicted') GROUP BY dbprimary_acc, stable_id");
+ $sth->execute();
+ print STDOUT "Writing out nucleotide links for database $dbname\n";
+ my $nucleotide_links = 0;
+ while ( ($ref_seq_accession,$ensembl_stable_id) = $sth->fetchrow_array() )
+ {
+ $link_no ++;
+my $link = " <Link>
+ <LinkId>$link_no</LinkId>
+ <ProviderId>7853</ProviderId>
+ <ObjectSelector>
+ <Database>$entrez_db</Database>
+ <ObjectList>
+ <Query>$ref_seq_accession</Query>
+ </ObjectList>
+ </ObjectSelector>
+ <ObjectUrl>
+ <Base>&base.url;</Base>
+ <Rule>$ensembl_stable_id</Rule>
+ </ObjectUrl>
+ </Link>\n";
+ {
+ use bytes;
+ my $byte_size = length($link);
+ $file_size += $byte_size;
+ }
+ #each file has a limit of 20Mb
+ if ($file_size >= 19900000) {
+ $number_of_files ++;
+ new_file();
+ }
+ print FH $link;
+ $nucleotide_links ++;
+ }
+
+ $sth->finish();
+ my $message = "Written out $nucleotide_links nucleotide links for database $dbname";
+ if ($nucleotide_links > 0) {
+ $message .= " in file(s):\n";
+ for (my $i = $current_file_no; $i <= $number_of_files; $i++) {
+ $message .= $out_file . "_" . "$i\n";
+ }
+ } else {
+ $message .= "\n";
+ }
+ print STDOUT $message;
+
+ #get protein data
+ $current_file_no = $number_of_files;
+ $entrez_db = "Protein";
+ $sth = $db->prepare("SELECT dbprimary_acc, stable_id FROM object_xref o INNER JOIN xref x on o.xref_id = x.xref_id INNER JOIN external_db e on e.external_db_id =x.external_db_id INNER JOIN translation_stable_id on ensembl_id = translation_id WHERE db_name in ('RefSeq_peptide', 'RefSeq_peptide_predicted') group by dbprimary_acc, stable_id");
+ $sth->execute();
+ print STDOUT "Writing out protein links for database $dbname\n";
+ my $protein_links = 0;
+ while ( ($ref_seq_accession,$ensembl_stable_id) = $sth->fetchrow_array() )
+ {
+ $link_no ++;
+my $link = " <Link>
+ <LinkId>$link_no</LinkId>
+ <ProviderId>7853</ProviderId>
+ <ObjectSelector>
+ <Database>$entrez_db</Database>
+ <ObjectList>
+ <Query>$ref_seq_accession</Query>
+ </ObjectList>
+ </ObjectSelector>
+ <ObjectUrl>
+ <Base>&base.url;</Base>
+ <Rule>$ensembl_stable_id</Rule>
+ </ObjectUrl>
+ </Link>\n";
+ {
+ use bytes;
+ my $byte_size = length($link);
+ $file_size += $byte_size;
+ }
+ #each file has a limit of 20Mb
+ if ($file_size >= 19900000) {
+ $number_of_files ++;
+ new_file();
+ }
+ print FH $link;
+ $protein_links ++;
+ }
+
+ $sth->finish();
+ $message = "Written out $protein_links protein links for database $dbname";
+ if ($protein_links > 0) {
+ $message .= " in file(s):\n";
+ for (my $i = $current_file_no; $i <= $number_of_files; $i++) {
+ $message .= $out_file . "_" . "$i\n";
+ }
+ } else {
+ $message .= "\n";
+ }
+ print STDOUT $message;
+ }
+
+ $db->disconnect();
+ print FH "</LinkSet>";
+ close FH;
+}
+sub usage {
+ print STDERR <<EOF
+
+ Usage: generate_LinkOut options
+ -dbpattern database name pattern
+ -out_file output resource file name, default 'resources'
+ -config_file should contain one or more lines with: host user port(optional), e.g. ens-staging1 ensro
+EOF
+;
+ exit;
+}
+
+sub new_file
+{
+ if ($number_of_files > 1) {
+ print FH "</LinkSet>";
+ close FH;
+ }
+ my $file_name = $out_file . $number_of_files . '.xml';
+ open( FH, ">$file_name" ) or die("Can't open $file_name\n");
+ print FH $header;
+ $file_size = $header_size;
+}
+
+
diff --git a/misc-scripts/link_out/linkOut_config.txt b/misc-scripts/link_out/linkOut_config.txt
new file mode 100644
index 0000000000..6d0bb9e41f
--- /dev/null
+++ b/misc-scripts/link_out/linkOut_config.txt
@@ -0,0 +1,2 @@
+ens-staging1 ensro
+ens-staging2 ensro
--
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