#!/usr/bin/perl #INPUT #Check for GET method and decode (standard method) if ($ENV{'REQUEST_METHOD'} eq 'GET') { $buffer = $ENV{'QUERY_STRING'}; #making list of keyword-value pair @pairs = split(/&/, $buffer); foreach $pair (@pairs) { ($name, $value) = split(/=/, $pair); #translate "+" to space $value =~ tr/+/ /; #decipher ASCI hexadecimal escaped characters $value =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg; #add the pair to a list keyed on the name of the variable $contents{$name} = $value; }} ############################################################################# #PROCESSING #check for which button is pressed $option = $contents{'option'}; if ($option eq "Lab Sites") { $query = $contents{'q'}; print < EOF exit; } # Duncan added this to handle hub if ($option eq "Linkhub") { $query = $contents{'q'}; print < EOF exit; } if ($option eq "Only this site (best)") { $query = "q=".$contents{'q'}; $hidden_fields = "pg=aq&what=web&t=submit&fmt="; $url = "http://search.yale.edu:8080/cgi-bin/query"; $host_spec = " AND ( host:bioinfo.mbb.yale.edu OR host:bioinfo2.mbb.yale.edu )"; } if ($option eq "This + related site") { $query = "q=".$contents{'q'}; $hidden_fields = "pg=aq&what=web&t=submit&fmt="; $url = "http://www.altavista.digital.com/cgi-bin/query"; $host_spec = " AND ( host:bioinfo.mbb.yale.edu OR host:bioinfo2.mbb.yale.edu OR url:hyper.stanford.edu/~mbg)"; } if ($option eq "Text on this site") { $query = "q=".$contents{'q'}; $hidden_fields = "pg=aq&what=web&t=submit&fmt="; #$url = "http://www.altavista.digital.com/cgi-bin/query"; $url = "http://www.altavista.com/web/results"; $host_spec = " ( host:www.gersteinlab.org OR host:bioinfo.mbb.yale.edu OR host:bioinfo2.mbb.yale.edu OR host:bioinfo5.mbb.yale.edu OR host:www.molmovdb.org OR host:www.pseudogene.org OR host:www.genecensus.org OR host:networks.gersteinlab.org OR host:spine.nesg.org OR host:hub.gersteinlab.org OR host:hub.gersteinlab.org OR host: hub.nesg.org )"; if ($contents{'q'} !~ m/^\s*$/) { $host_spec = " AND" . $host_spec; } } if ($option eq "Gene or PDB ID") { $id = $contents{'q'}; $query = "id=".$id; #for pdb search, q is not used for query $hidden_fields = ""; $url = "http://bioinfo.mbb.yale.edu/genome/search/superlink.cgi"; $host_spec = ""; } if ($option eq "Pages linking us") { $query = "q=".$contents{'q'}; $hidden_fields = "pg=aq&what=web&t=submit&fmt="; #$url = "http://www.altavista.digital.com/cgi-bin/query"; $url = "http://www.altavista.com/web/results"; $host_spec = " ( link:bioinfo.mbb.yale.edu OR link:gersteinlab.org OR link:bioinfo.csb.yale.edu OR link:www.molmovdb.org OR link:www.pseudogene.org OR link:www.genecensus.org OR link:networks.gersteinlab.org OR link:spine.nesg.org OR link:hub.gersteinlab.org OR link:hub.nesg.org ) NOT ( host:hyper.stanford.edu OR host:bioinfo.mbb.yale.edu OR host:gersteinlab.org OR host:molmovdb.org OR host:pseudogene.org OR host:genecensus.org OR networks.gersteinlab.org OR host:nesg.org OR host:hub.gersteinlab.org OR host:hub.nesg.org )"; if ($contents{'q'} !~ m/^\s*$/) { $host_spec = " AND" . $host_spec; } #" AND (link:bioinfo.mbb.yale.edu OR link:gersteinlab.org OR link:bioinfo2.mbb.yale.edu OR link:bioinfo5.mbb.yale.edu OR link:bioinfo.csb.yale.edu) NOT (host:hyper.stanford.edu OR host:bioinfo.mbb.yale.edu OR host:gersteinlab.org OR host:bioinfo2.mbb.yale.edu OR host:bioinfo5.mbb.yale.edu OR host:hyper OR host:bioinfo.csb OR host:aragorn)"; #" AND (link:bioinfo.mbb.yale.edu OR link:bioinfo2.mbb.yale.edu OR link:bioinfo5.mbb.yale.edu OR link:bioinfo.csb.yale.edu) AND ( NOT host:hyper.stanford.edu ) AND( NOT host:bioinfo.mbb.yale.edu ) AND ( NOT host:bioinfo2.mbb.yale.edu ) AND ( NOT host:bioinfo5.mbb.yale.edu ) AND ( NOT host:hyper ) AND ( NOT host:bioinfo.csb ) AND ( NOT host:bioinfo2.csb ) AND ( NOT host:aragorn )"; } if ($option eq "PDB search") { $id = $contents{'q'}; $query = "pdb=".$id; #for pdb search, q is not used for query $hidden_fields = ""; $url = "http://bioinfo.mbb.yale.edu/pdbreport.cgi"; $host_spec = ""; #check to see if the id is valid $id =~ s/\s//g; #get rid of white space if ((length($id) != 4) #should have only 4 characters or ((substr($id,0,1) =~ tr/0-9//) != 1) #first chara should be a digit or (($id =~ tr/a-zA-Z//) != 3)) #the next 3 should be all letters { #Create html document to tell the user that the format is wrong #print this MIME data no matter what print "Content-type: text/html\n\n"; print < Please use the correct PDB format: [0-9][A-Z][A-Z][A-Z] HTML exit; } } if ($option eq "SCOP search") { $id = $contents{'q'}; $query = "sid=".$id; #for pdb search, q is not used for query $hidden_fields = ""; $url = "http://bioinfo.mbb.yale.edu/pdbreport.cgi"; $host_spec = ""; #check to see if the id is valid $id =~ s/\s//g; #get rid of white space if ((length($id) != 7) #should have only 4 characters or ((substr($id,0,1) ne "d")) or ((substr($id,1,1) =~ tr/0-9//) != 1) #first chara should be a digit ) { #Create html document to tell the user that the format is wrong #print this MIME data no matter what print "Content-type: text/html\n\n"; print < Please use the correct PDB format: [0-9][A-Z][A-Z][A-Z] HTML exit; } } #encode $host_spec to format acceptible by search engines $host_spec =~ s/(\W)/sprintf("%%%x", ord($1))/eg; $host_spec =~ s/%20/\+/g; #optional: space to +; just to look good $host_spec =~ s/%2e/\./g; #optional: fullstop as .; just to look good #make the final url to send to the search engine $hidden_fields .= "&" if ($hidden_fields); $url .= "?$hidden_fields$query$host_spec"; #server redirection to the required search engine print "Location: $url", "\n\n"; exit (0);