#!/usr/bin/perl -w $file = $ARGV[0]; if(!defined($file)) {exit} $outfile = $file; $outfile =~ s/ - EMBOSS[.]htm/.wiki/g; open (OUT, ">/cygdrive/h/wikifix/$outfile") || die "Cannot open '$outfile'"; %author = ("ableasby" => "Bleasby", "price" => "Rice", "ilongden" => "Longden", "mschuster" => "Schuster", ); %types = ("Ione" => "Short", # headers on one line "Ihtml" => "", "Itable" => "Options", "Usage" => "Example", "Input" => "Input", "Output" => "Output", "History" => "History", "Comment" => "Comment", "Isee" => "Seealso" ); %names = ("Alignformats" => "AlignFormats", "Assemblyformats" => "AssemblyFormats", "Codonformats" => "CodonFormats", "Featformats" => "FeatFormats", "Ontologyformats" => "OntologyFormats", "Reportformats" => "ReportFormats", "Resourceformats" => "ResourceFormats", "Seqformats" => "SeqFormats", "Seqfeatformats" => "SeqfeatFormats", "Taxonformats" => "TaxonFormats", "Textformats" => "TextFormats", "Urlformats" => "UrlFormats", "Variationformats" => "VariationFormats", "Assemblyinformats" => "AssemblyInFormats", "Codoninformats" => "CodonInFormats", "Featinformats" => "FeatInFormats", "Ontologyinformats" => "OntologyInFormats", "Resourceinformats" => "ResourceInFormats", "Seqinformats" => "SeqInFormats", "Seqfeatinformats" => "SeqfeatInFormats", "Taxoninformats" => "TaxonInFormats", "Textinformats" => "TextInFormats", "Urlinformats" => "UrlInFormats", "Variationformats" => "VariationFormats", "Gcfiles" => "GeneticCodeFiles", "Localfiles" => "LocalFiles", "Graphicsdevices" => "GraphicsDevices", "Drcat" => "Drcat", "Edam" => "Edam", "Go" => "Go", "Taxon" => "Taxon", "Jaspfiles" => "JasparFiles", "Refiles" => "RebaseFiles", "Jison-programs" => "JonIsonPrograms", ); use English; $text = ""; while (<>) { s/^[ \t]+//; $text .= $_; } $text =~ s/^.*(([^<]+)<\/h1>\n//osm; # remove all to start of mediawiki print STDERR "Page true name $1\n"; $text =~ s/^.*?\n([^\n]+)/$1/osm; # remove all to first heading $text =~ s///gosm; $text =~ s/<\/span><\/span>/\n/gosm; $text =~ s/<\!--\s*NewPP limit report[^>]*>//gosm; # remove biblio comments $text =~ s/<\!--\s*Saved in parser cache.*//gosm; # remove all from start of google footer $text =~ s/\s*([^<]+)<\/span>/$1/gosm; # clean up headings #header tages removed $text =~ s/(<\/?[Hh][Tt][Mm][Ll]>)//gosm; $text =~ s/(<\/?[Bb][Oo][Dd][Yy][^>]*?>)//gosm; $text =~ s/(<[Aa]\s+name\s*=\s*\"([^\"]+)[^>]+>)[^<]*<\/[Aa]>//gosm; # phylip doc links $text =~ s/<[Aa]\s+href\s*=\s*\"([^\/\".]+\.html)[^>]+>([^<]+)<\/[Aa]>/[http:\/\/evolution.genetics.washington.edu\/phylip\/doc\/$1 $2]/gosm; # other links $text =~ s/<[Aa]\s+href\s*=\s*\"\/wiki\/([^\"]+)[^>]+>\s*([^<]+)<\/[Aa]>/[[$1| $2]]/gosm; $text =~ s/<[Aa]\s+href\s*=\s*\"([Hh]?[FfTt][Tt][Pp]:[^\"]+)[^>]+>([^<]+)\s*<\/[Aa]>/[$1 $2]/gosm; $text =~ s/<[Aa]\s+href\s*=\s*\"([Mm]?[Aa][Ii][Ll][Tt][Oo]:[^\"]+)[^>]+>([^<]+)\s*<\/[Aa]>/[$1 $2]/gosm; $text =~ s/<[Aa]\s+href\s*=\s*\"([^\"]+)[^>]+>([^<]+)\s*<\/[Aa]>/[[$1| $2]]/gosm; # headers on one line $text =~ s/(<[Hh]\d>)\s*\n\s*/$1/gosm; $text =~ s/\n(<\/[Hh]\d>)/$1/gosm; # remove CSS divisions $text =~ s/<\/[Dd][Ii][Vv]>//gosm; # remove rulers $text =~ s/<[Hh][Rr]>//gosm; # header levels to wiki syntax $text =~ s/<[Hh]1>(.*?)<\/[Hh]1>/==$1==/gosm; $text =~ s/<[Hh]2>(.*?)<\/[Hh]2>/==$1==/gosm; $text =~ s/<[Hh]3>(.*?)<\/[Hh]3>/===$1===/gosm; $text =~ s/<[Hh]4>(.*?)<\/[Hh]4>/====$1====/gosm; # paragraphs to extra newlines at start $text =~ s/<[Pp]>/\n/gosm; # remove table row end markings $text =~ s/^(<\/[Tt][RrDdHh]>)+\n//gosm; $text =~ s/<\/[Tt][RrDdHh]>//gosm; $text =~ s/^(<\/[Cc][Aa][Pp][Tt][Ii][Oo][Nn]>)+\n//gosm; $text =~ s/<\/[Cc][Aa][Pp][Tt][Ii][Oo][Nn]>//gosm; # remove end-of-paragraph $text =~ s/<\/[Pp]>//gosm; # breaks $text =~ s/(<\/?[Bb][Rr][^>]*>)/\n/gosm; # bold text $text =~ s/(<\/?[Bb][^>]*>)/'''/gosm; # emphasis = bold $text =~ s/(<\/?[Ee][Mm]>)/'''/gosm; # italic $text =~ s/(<\/?[Ii]>)/''/gosm; # remove empty newlines after list tags $text =~ s/(<\/?[Ll][Ii]>)\n/$1/gosm; $text =~ s/(<\/[Ll][Ii]>)//gosm; $text =~ s/(<\/?[Dd][DdTt]>)\n/$1/gosm; $text =~ s/(<\/[Dd][DdTt]>)//gosm; $text =~ s/([^\n])(<[Tt][HhDd][^>]*>)/$1\n$2/gosm; # Now process the text line-by-line $i=0; $pre = 0; $head=0; $blank=0; $table = 0; $list = ""; while ($text =~ /.*?\n/gos) { $t = $MATCH; if($t =~ s/<[Hh][Ee][Aa][Dd]>//gosm) {$head=1} if($t =~ s/<\/[Hh][Ee][Aa][Dd]>//gosm) {$head=0;next} if($t =~ s///gosm) {$head=1} if($t =~ s///gosm) {$head=0;next} if($head) {next} if($t =~ s/<\/[Tt][Aa][Bb][Ll][Ee][^>]*>//gosm) { $table = 0; print OUT "|}\n"; } if($t =~ s/<[Tt][Aa][Bb][Ll][Ee]([^>]*)>//gosm) { $table = 1; $rest = $1; $resttext = ""; if($rest =~ /sortable/) {$resttext = " sortable"} print OUT "\n{| class=\"wikitable$resttext\" style=\"background:#ccccff\" border=\"2\"\n"; } if($t =~ s/<\/[OoUuDd][Ll]>//gosm) {$list = ""} if($t =~ s/<[Uu][Ll]>//gosm) {$list = "u";$nlist=0} if($t =~ s/<[Oo][Ll]>//gosm) {$list = "o";$nlist=0} if($t =~ s/<[Dd][Ll]>//gosm) {$list = "d";$nlist=0} if($t =~ s/<[Pp][Rr][Ee]>//gosm) {$pre = 1} if($t =~ s/<\/[Pp][Rr][Ee]>//gosm) {$pre = 0} if($t =~ /<[!]--[\#]include file=\"([^\"]+)\" -->/gosm){ $ifile = $1; if($ifile =~ /inc\/([^.]+)[.]address/){ $aname = $1; if(defined($author{$aname})){$aname = $author{$aname}} else {$aname = ucfirst($aname)} $t = "\{\{:Appinc:Address$aname\}\}\n"; } elsif($ifile =~ /inc\/target([^.]*)[.]itxt/){ $tgtname = ucfirst($1); $t = "\{\{:Appinc:Target$tgtname\}\}\n"; } elsif($ifile =~ /inc\/([^.]+)[.]ihelp/){ $t = ""; } elsif($ifile =~ /inc\/([^.]+)[.](.*)/){ $name = ucfirst($1); $type=ucfirst($2); if(defined($names{$name})){$name = $names{$name}} if(defined($types{$type})){$type = $types{$type}} if($type eq "Seealso") { print OUT "==See also==\n"; } $t = "\{\{:Appinc:$type$name\}\}\n"; } } if(!$pre & $t =~ /^\n$/) {$blank++} else{$blank=0} $i++; if($blank > 1){next} if($blank == 1 && $list ne ""){next} # print OUT "$i:"; if($list ne "") {$t =~ s/\n/ /} if($pre) {print OUT " "} if($t =~ s/<[Tt][Rr]>//gosm) { if($table) { print OUT "|-"; $table = 2; } } if($t =~ s/<[Cc][Aa][Pp][Tt][Ii][Oo][Nn]>//gosm) { if($table) { print OUT "|+"; $table = 2; } } if($t =~ s/<[Tt][Hh]([^>]*)>//gosm) { if($table) { $rest = $1; $resttext = ""; if($rest =~ /colspan=\"(\d+)\"/) { $resttext .= " colspan=\"$1\""; } if($rest =~ /class=\"unsortable"/) { $resttext .= " class=\"unsortable\""; } if($rest =~ /background:(#[0-9a-fA-F]+)/) { $resttext .= " style=\"background:$1\""; } if($resttext ne "") {$resttext .= "|"} print OUT "!$resttext "; $table = 4; } } if($t =~ s/<[Tt][Dd]>//gosm) { if($table) { print OUT "| "; $table = 3; } } if($t =~ s/<[Ll][Ii]>//gosm) { if($nlist++){print OUT "\n"} if($list eq "u") {print OUT "* "} elsif($list eq "o") {print OUT "# "} } if($t =~ s/<[Dd][Tt]>([^<]*)//gosm) { if($nlist++){print OUT "\n"} if($list eq "d") {print OUT "; $1"} } if($t =~ s/<[Dd][Dd]>//gosm) { if($nlist++){print OUT "\n"} if($list eq "d") {print OUT ": "} } if($nlist && $list eq "") {print OUT "\n";$nlist=0;} print OUT "$t"; }