#!/usr/bin/perl -- # -*-Perl-*- =head1 NAME dbfetch - generic CGI program to retrieve biological database entries in various formats and styles (using SRS) =head1 SYNOPSIS # URL examples: # prints the interactive page with the HTML form http://www.ebi.ac.uk/Tools/dbfetch/dbfetch # for backward compatibility, implements <ISINDEX> # single entry queries defaulting to EMBL sequence database http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?J00231 # retrieves one or more entries in default format # and default style (html) # returns nothing for IDs which are not valid http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?id=J00231.1,hsfos,bum # retrieve entries in fasta format without html tags http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=fasta&style=raw&id=J00231,hsfos,bum # retrieve a raw Ensembl entry http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ensembl&style=raw&id=AL122059 =head1 DESCRIPTION This program generates a page allowing a web user to retrieve database entries from a local SRS in two styles: html and raw. Other database engines can be used to implement te same interfase. At this stage, on unique identifier queries are supported. Free text searches returning more than one entry per query term are not in these specs. In its default setup, type one or more EMBL accession numbers (e.g. J00231), entry name (e.g. BUM) or sequence version into the seach dialog to retieve hypertext linked enties. Note that for practical reasons only the first 50 identifiers submitted are processed. Additional input is needed to change the sequence format or suppress the HTML tags. The styles are html and raw. In future there might be additional styles (e.g. xml). Currently XML is a 'raw' format used by Medline. Each style is implemented as a separate subroutine. =head1 MAINTANENCE A new database can be added simply by adding a new entry in the global hash %IDS. Additionally, if the database defines new formats add an entry for each of them into the hash %IDMATCH. After modifying the hash, run this script from command line for some sanity checks with parameter debug set to true (e.g. dbfetch debug=1 ). Finally, the user interface needs to be updated in the L<print_prompt> subroutine. =head1 VERSIONS Version 3 uses EBI SRS server 6.1.3. That server is able to merge release and update libraries automatically which makes this script simpler. The other significant change is the way sequence versions are indexed. They used to be indexed together with the string accession (e.g. 'J00231.1'). Now they are indexed as integers (e.g. '1'). Version 3.1 changes the command line interface. To get the debug information use attribute 'debug' set to true. Also, it uses File::Temp module to create temporary files securely. Version 3.2 fixes fasta format parsing to get the entry id. Version 3.3. Adds RefSeq to the database list. Version 3.4. Make this compliant to BioFetch specs. =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =cut # Let the code begin... $VERSION = '3.4'; $DATE = '28 Jan 2002'; use CGI "standard"; #use POSIX; use CGI::Carp qw/ fatalsToBrowser /; use File::Temp qw/ tempfile tempdir /; use strict; no strict "refs"; use constant MAXIDS => 50; use constant TMPDIR => '/usr/tmp'; use vars qw( $VERSION $DATE %DBS %STYLES $RWGETZ $RGETZ %IDMATCH %IDLIST $XEMBL $FH ); BEGIN { # paths to SRS binaries $RWGETZ = '/ebi/srs/srs/bin/osf_5/wgetz -e'; $RGETZ = '/ebi/srs/srs/bin/osf_5/getz -e'; $XEMBL = "cd /ebi/www/pages/cgi-bin/xembl/; ./XEMBL.pl"; #$EMBOSSDIR = '/ebi/services/pkgs/emboss/bin'; # RE matching the unique ID in the db entry # - key is the # - put the id string in parenthesis %IDMATCH = ( # 123 embl => 'ID (\w+)', fasta => '>\w+.(\w+)', medlinefull => '[\n><]MedlineID. ?(\w+)', swissprot => 'ID (\w+)', pdb => '.{62}(\w+)', bsml => 'DUMMY', agave => 'DUMMY', refseq => 'LOCUS ([\w_]+)' ); %DBS = ( embl => { fields => ['id', 'acc'], version => 'sv', # name of the SRS field format => { default => 'embl', embl => 1, fasta => 'FastaSeqs', bsml => 1, agave => 1 } }, medline => { fields => ['id'], format => { default => 'medlinefull', # medlineref => 'MedlineRef', medlinefull => 'MedlineFull' } }, ensembl => { fields => ['id'], format => { default => 'embl', embl => 1, fasta => 'FastaSeqs' } }, swall => { fields => ['id', 'acc'], format => { default => 'swissprot', swissprot => 1, fasta => 'FastaSeqs' } }, pdb => { fields => ['id'], format => { default => 'pdb', pdb => '1' } }, refseq => { fields => ['id', 'acc'], format => { default => 'refseq', refseq => 1, fasta => 'FastaSeqs' } } #add more databases here... ); %STYLES = ( html => 1, raw => 1 ); %IDLIST = (); #redundancy check list built during the execution } my $q = new CGI; # sanity checks if the script is running from command line # and debug parameter is set. my $debug = protect($q->param('debug')) if $q->param('debug'); &debugging if not $q->user_agent and $debug; if ( $q->param('id') or $q->param('keywords') ) { # pacify input strings my $value; $value = protect($q->param('id')) if $q->param('id'); $value = protect($q->param('keywords')) if $q->param('keywords'); my $db = lc protect($q->param('db')); # let's keep the case lower my $format = lc protect($q->param('format')); my $style = lc protect($q->param('style')); # check input and set defaults $style ||= 'html'; # default style input_error($q, $style, "2 Unknown style [$style].") unless $STYLES{$style}; $db ||= 'embl'; # default db input_error($q, $style, "1 Unknown database [$db].") unless $DBS{$db}; $format ||= $DBS{$db}{format}{default}; # default format input_error($q, $style, "3 Format [$format] not known for database [$db]") unless $DBS{$db}{format}{$format}; $format = $DBS{$db}{format}{default} if $format eq 'default'; # If people choose Bsml or AGAVE, DB can only be 'embl' input_error($q, $style, "1 Unknown database [$db].") if ($format eq 'bsml' or $format eq 'agave') and $db ne 'embl'; # If people choose Bsml or AGAVE, internal style has to be xml . Make it so. $style = ($format =~ /(bsml|agave)/i) ? 'xml' : $style; if ($style eq 'html') { print $q->header(-type => 'text/html', -charset => 'UTF-8'); } elsif ($style eq 'raw') { print "Content-Type: text/plain; charset=UTF-8\n\n"; } $FH = tempfile('dbfetchXXXXXX', DIR => TMPDIR, UNLINK => 1 ); #automatic unlinking # Check the number of IDs my @ids = split (/ /, $value); input_error($q, $style, "6 Too many IDs [". scalar @ids. "]. Max [". MAXIDS. "] allowed.") if scalar @ids > MAXIDS; # XEMBL cannot 'glue' single entries due to XML setup #- we need to send things in one go. if ($style eq 'xml') { &xml($format, @ids); } else { my $counter; foreach my $id (@ids) { &$style($db, $id, $format); } no_entries($q, $value) if $style eq 'html' and tell($FH) == 0; } seek $FH, 0, 0; print '<pre>' if $style eq 'html'; print $_ while <$FH>; } else { print_prompt($q); } =head2 print_prompt Title : print_prompt Usage : Function: Prints the default page with the query form to STDOUT (Web page) Args : Returns : =cut sub print_prompt { print $q->header(), $q->start_html(-title => 'DB Entry Retrieval', -bgcolor => 'white', -author => 'heikki-at-bioperl-dot-org' ), '<IMG align=middle SRC="/icons/ebibanner.gif">', $q->h1('Generic DB Entry Retrieval'), $q->p("This page allows you to retrieve up to ". MAXIDS . " entries at the time from various up-to-date biological databases."), $q->p("For EMBL, enter an accession number (e.g. J00231) or entry name (e.g. BUM) or a sequence version (e.g. J00231.1), or any combination of them separated by a non-word character into your browser's search dialog. SWALL examples are: fos_human, p53_human. For short Ensembl entries, try : AL122059, AL031002, AL031030 . 'Random' Medline entry examples are: 20063307, 98276153. PDB entry examples are: 100D, 1FOS. Try NM_006732 for RefSeq. Only one copy of the latest version of the entry is returned."), $q->hr, $q->startform, $q->popup_menu(-name => 'db', -values => ['EMBL', 'SWALL', 'PDB', 'Medline', 'Ensembl', 'RefSeq' ]), $q->textfield(-name => 'id', -size => 40, -maxlength => 1000), $q->popup_menu(-name => 'format', -values => ['default','Fasta','bsml','agave']), $q->popup_menu(-name => 'style', -values => ['html','raw']), $q->submit('Retrieve'), $q->endform, $q->hr, $q->h2('Direct access'), $q->p('For backward compatibility, the script defaults to EMBL:'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?J00231"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?J00231</a>'), $q->p('but the preferred way of calling it is:'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?id=J00231.1,hsfos,bum"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?id=J00231.1,hsfos,bum</a>'), $q->p('which can be extended to retrieve entries in alternative sequence formats and other databases:'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=swall&format=fasta&id=fos_human"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=swall&format=fasta&id=fos_human</a>'), $q->p('Set style to <code>raw</code> to retrieve plain text entries for computational purposes and saving to disk:'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&id=21131735"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&id=21131735</a>'), $q->p('There is now the possibility to retrieve EMBL sequences formatterd into two XML standards: Bsml (Bioinformatic Sequence Markup Language - from Labbook, Inc.) or as AGAVE (Architecture for Genomic Annotation, Visualisation, and Exchange - from Labbook, Inc.). To do this, use the formats \'bsml\' or \'agave\', as follows:'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=bsml&id=J00231"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=bsml&id=J00231</a><br>'), $q->code('<A href="http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=agave&id=J00231"> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=agave&id=J00231</a>'), $q->p("Version numbers are not supported with the XML retrieval."), $q->hr, $q->address("Version $VERSION, $DATE, <a href=\"mailto:support\@ebi.ac.uk\">support\@ebi.ac.uk</a>"), $q->end_html, "\n" ; } =head2 protect Title : protect Usage : $value = protect($q->param('id')); Function: Removes potentially dangerous characters from the input string. At the same time, converts word separators into a single space character. Args : scalar, string with one or more IDs or accession numbers Returns : scalar =cut sub protect { my ($s) = @_; $s =~ s![^\w\.\_]+! !g; # allow version numbers with '.' & RefSeq IDs with '_' $s =~ s|^\W+||; $s =~ s|\W+$||; return $s; } =head2 input_error Title : input_error Usage : input_error($q, 'html', "Error message"); Function: Standard error message behaviour Args : reference to the CGI object scalar, string to display on input error. Returns : scalar =cut sub input_error { my ($q, $style, $s) = @_; if ($style eq 'html' ) { print $q->header, $q->start_html(-title => 'DB Entry Retrieval: Input error', -bgcolor => 'white' ), "<h2>ERROR in input:<h2>$s\n", $q->end_html, "\n"; } else { print "Content-type: text/plain\n\n", "ERROR $s\n"; } exit 0; } =head2 no_entries Title : no_entries Usage : no_entries($q, "Message"); Function: Standard behaviour when no entries found Args : reference to the CGI object scalar, string to display on input error. Returns : scalar =cut sub no_entries { my ($q, $value) = @_; print $q->start_html(-title => 'DB Entry Retrieval: Input warning', -bgcolor => 'white' ), "<h2>Sorry, your query retrieved no entries.</h2>", "Entries with [$value] where not found.", "Please go back or press <a href=\"dbfetch\"><b>here</b></a> to try again", $q->end_html, "\n"; exit 0; } =head2 raw Title : raw Usage : Function: Retrieves a single database entry in plain text Args : scalar, an ID scaler, format Returns : scalar =cut sub raw { my ($db, $value, $format) = @_; my ($srsq, $qdb, $entry, $id); my ($seqformat) = ''; $seqformat = '-view '. $DBS{$db}{format}{$format} if $format ne $DBS{$db}{format}{default}; my $version = ''; $value =~ /(.+)\.(.+)/; $version = $2 if $2; $value = $1 if $1; # main db $qdb = $db; $srsq = ''; foreach my $field (@{$DBS{$db}{fields}}) { $srsq .= " [$qdb-$field:$value] |"; } chop $srsq; # if database supports versions (EMBL, GenBank, RefSeq...) if ($version) { my $vfname = $DBS{$db}{version}; $srsq = "[$qdb-$vfname:$version] & (". $srsq. ")" } # print "rsh srs $RGETZ $seqformat $srsq\n"; $entry = `rsh srs "$RGETZ $seqformat '$srsq'"`; $entry =~ s|EMBL[^\n]+\n||; $entry =~ s|^\s+||g; $entry =~ s|\s+$|\n|g; my $idmatch = $IDMATCH{$format}; ($id) = $entry =~ /$idmatch/; # die if ID not found input_error(' ', 'raw', "5 ID [$value] not found in database [$db].") unless $id; # my $tmp = substr($entry, 0, 20); # print "Entry:$tmp\n"; # print "-----id=$id---\$1=$1----idmatch=$idmatch=format=$format=\n"; # print $FH $entry unless $IDLIST{$id}; $IDLIST{$id} = 1; } =head2 html Title : html Usage : Function: Retrieves a single database entry with HTML hypertext links in place. Limits retieved enties to ones with correct version if the string has '.' in it. Args : scalar, a UID scalar, format Returns : scalar =cut sub html { my ($db, $value, $format) = @_; my ($srsq, $qdb, $entry, $id, $idmatch); my ($seqformat) = ''; $seqformat = '-view '. $DBS{$db}{format}{$format} if $format ne $DBS{$db}{format}{default}; my $version = ''; $value =~ /(.+)\.(.+)/; $version = $2 if $2; $value = $1 if $1; # SWALL plain format at EBI $seqformat .= ' -vn 2 ' if $db eq 'swall' or $db eq 'refseq'; $qdb = $db; $srsq = ''; foreach my $field (@{$DBS{$db}{fields}}) { $srsq .= " [$qdb-$field:$value] |"; } chop $srsq; # if database supports versions (EMBL...) if ($version) { my $vfname = $DBS{$db}{version}; $srsq = "[$qdb-$vfname:$version] & (". $srsq. ")" } # print "rsh srs $RWGETZ $seqformat $srsq\n"; ### '-id EBISRS' is (hopefully) a temporary addtion until SRS HTML output is fixed $entry = `rsh srs "$RWGETZ $seqformat '$srsq'"`; return if $entry =~ /SRS error/; $entry =~ s|^Content-type:[^\n]+\n||; $entry =~ s|\n<A HREF[^\n]+\n||; $entry =~ s|<A +HREF=\"?wgetz|<A HREF=http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz|g; #"\ $entry =~ s/\+-e\"/\+-e/g; #" $entry =~ s|<BR>||g; $entry =~ s|</?pre>||g; $entry =~ s|\n+|\n|g; $entry =~ s|^\n+||g; $idmatch = $IDMATCH{$format}; ($id) = $entry =~ /$idmatch/; # my $tmp = substr($entry, 0, 20); # print "Entry:$tmp\n"; # print "-----id=$id---\$1=$1----idmatch=$idmatch=format=$format=\n"; print $FH $entry unless $IDLIST{$id}; $IDLIST{$id} = 1; } =head2 xml Title : xml Usage : Function: Retrieves an entry formatted as XML Args : array, UID scalar, format Returns : scalar =cut sub xml { my ($format, @ids) = @_; my ($entry, $id, $content, $counter, $reg); $content = ($ENV{'HTTP_USER_AGENT'} =~ /MSIE/) ? "Content-type: text/xml\n\n" : "Content-type: text/plain\n\n"; $entry = "--format ".(($format eq "bsml") ? "Bsml" : "sciobj") . " " . join (" ", @ids); $entry = `rsh mercury "$XEMBL $entry"`; $reg = (($format eq "bsml") ? '<Sequence id=' : '<contig length-'); $counter++ while $entry =~ /($reg)/g; foreach my $idl (@ids) { input_error($q, " ", "5 ID [$idl] not found in database [embl].") if ($format eq "bsml" && $entry =~ "NOT EXIST: $idl") || ($format eq "agave" && $entry =~ "NOT FOUND: $idl") } print $FH ($content . $entry); } =head2 debugging Title : debugging Usage : 'perl dbfetch' Function: Performs sanity checks on global hash %IDS when this script is run from command line. %IDS holds the description of formats and other crusial info for each database accessible through the program. Note that hash key 'version' is not tested as it should only be in sequence databases. Args : none Returns : error messages to STDOUT =cut sub debugging { foreach my $db (keys %DBS) { my $status = 1; # field print "ERROR: [$db]: no SRS fields defined.". " Give an array of field names?\n" and $status = 0 unless $DBS{$db}{fields}; print "ERROR: [$db]: SRS fields are not defined as an array.\n" and $status = 0 unless ref $DBS{$db}{fields} eq 'ARRAY'; # format print "ERROR: [$db]: no formats defined.\n" and $status = 0 unless $DBS{$db}{format}; print "ERROR: [$db]: no default format defined.\n" and $status = 0 unless $DBS{$db}{format}{default}; my $format = $DBS{$db}{format}{default}; print "ERROR: [$db]: no format [$format] defined.". " You declared it as a default and only.\n" and $status = 0 unless $DBS{$db}{format}{$format}; foreach my $dbformat (keys %{$DBS{$db}{format}}) { print "ERROR: [$db]: format [$format] not defined in %IDMATCH.\n" and $status = 0 unless $IDMATCH{$dbformat} or $dbformat eq 'default'; } printf "%-12s%s", "[$db]", "OK\n" if $status; } exit; }