| 1 | #!/usr/bin/perl -w |
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| 2 | # switches for stringent coding and debugging |
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| 3 | |
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| 4 | # This program is an adapter between the ARB program package and the DSZM website. |
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| 5 | # It allows to run a taxonomic query using the web form offered by the DSZM via |
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| 6 | # the http-POST method implemented by the LWP package of perl. |
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| 7 | # Subsequent modification of relative URLs into absolute one allows allows the browser |
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| 8 | # started by ARB to connect with the DSZM website. |
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| 9 | # (c) Lothar Richter Oct. 2003 |
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| 10 | |
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| 11 | use strict; |
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| 12 | use diagnostics; |
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| 13 | |
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| 14 | |
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| 15 | # script for automated information retrieval from DSZM |
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| 16 | |
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| 17 | |
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| 18 | # moduls in use |
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| 19 | use LWP::Simple; |
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| 20 | use HTTP::Request::Common qw(POST); |
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| 21 | use LWP::UserAgent; |
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| 22 | |
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| 23 | use File::Temp qw/ tempfile tempdir /; |
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| 24 | |
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| 25 | |
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| 26 | |
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| 27 | |
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| 28 | #die"code successful parsed and compiled\n"; |
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| 29 | |
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| 30 | |
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| 31 | |
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| 32 | |
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| 33 | my $errordocument = |
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| 34 | "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\"> |
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| 35 | <html> |
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| 36 | <head> |
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| 37 | <title>DSMZ Failure</title> |
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| 38 | </head> |
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| 39 | |
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| 40 | <body> |
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| 41 | <h1>DSZM Access Error</h1> |
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| 42 | <br/> |
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| 43 | You have given no search items! Please give at least on search item to access the taxonomic search tool at the DSMZ! |
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| 44 | |
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| 45 | <hr> |
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| 46 | <address><a href=\"mailto:\">Lothar Richter</a></address> |
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| 47 | <!-- Created: Mon Sep 8 14:23:58 CEST 2003 --> |
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| 48 | <!-- hhmts start --> |
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| 49 | Last modified: Mon Sep 8 14:25:42 CEST 2003 |
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| 50 | <!-- hhmts end --> |
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| 51 | </body> |
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| 52 | </html>"; |
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| 53 | |
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| 54 | my $TMPOUT; |
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| 55 | my $template = 'arbdsmz_XXXXXX'; |
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| 56 | (undef, $TMPOUT) = tempfile($template, OPEN => 0); |
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| 57 | $TMPOUT = $TMPOUT . ".html"; |
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| 58 | |
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| 59 | open (OUTPUT , "> $TMPOUT") or die "cannot open temporary input file $TMPOUT"; |
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| 60 | |
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| 61 | if (scalar(@ARGV) == 0) |
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| 62 | {print OUTPUT $errordocument; |
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| 63 | die("no search items given ! Give at least one item!");} |
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| 64 | ##print length(@ARGV)."\n"; |
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| 65 | my $item1 = shift() || ""; |
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| 66 | ##print $item1."\n"; |
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| 67 | my $item2 = shift() || ""; |
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| 68 | |
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| 69 | print STDERR "Searching for '$item1'\n"; |
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| 70 | print STDERR "Searching for '$item2'\n"; |
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| 71 | |
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| 72 | #-------------------------------------------------------------------------------- |
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| 73 | # begin of post-method emulations |
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| 74 | #-------------------------------------------------------------------------------- |
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| 75 | |
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| 76 | |
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| 77 | my $ua_selection = LWP::UserAgent ->new ; |
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| 78 | |
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| 79 | #$ua_selection -> agent ("UpdateAgent/0.1" . $ua_selection -> agent); |
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| 80 | |
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| 81 | ##my $req_selection = new HTTP::Request POST => $baseURL; |
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| 82 | my $req_selection = HTTP::Request -> new( POST => 'http://www.dsmz.de/cgi-bin/dsmzfind.pl'); |
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| 83 | ##my $req_selection = HTTP::Request -> new( POST => $baseURL); |
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| 84 | |
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| 85 | $req_selection->content_type('application/x-www-form-urlencoded'); |
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| 86 | # my $selection_content = 'VAR_DATABASE=bact&VAR_HITS=25&VAR_DSMZITEM=Escherichia&VAR_DSMZITEM2=coli&B1=Search'; |
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| 87 | my $selection_content = 'VAR_DATABASE=bact&VAR_HITS=25&VAR_DSMZITEM='."$item1".'&VAR_DSMZITEM2='."$item2".'&B1=Search'; |
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| 88 | |
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| 89 | $req_selection->content($selection_content); |
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| 90 | |
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| 91 | # Pass request to the user agent and get a response back |
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| 92 | my $TMPUSEROUT; |
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| 93 | (undef, $TMPUSEROUT) = tempfile($template, OPEN => 0); |
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| 94 | $TMPUSEROUT = $TMPUSEROUT . ".htm"; |
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| 95 | my $res_selection = $ua_selection -> request($req_selection, $TMPUSEROUT); |
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| 96 | |
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| 97 | |
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| 98 | |
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| 99 | # Check the outcome of the response |
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| 100 | if ($res_selection->is_success) {print $res_selection->content;} |
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| 101 | else {die "Bad luck this time, request failed\n";}; |
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| 102 | |
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| 103 | |
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| 104 | open (INPUT , "< $TMPUSEROUT") or die "cannot open input file $TMPUSEROUT"; |
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| 105 | |
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| 106 | |
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| 107 | my $htmlcontent; |
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| 108 | { |
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| 109 | local $/; |
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| 110 | $htmlcontent = <INPUT>; |
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| 111 | } |
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| 112 | ##print "$htmlcontent\n"; |
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| 113 | |
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| 114 | ##$htmlcontent =~ s{(.*HREF=")(\/w+)}{$1http:\/\/www.dszm.de$1}igm; ##" |
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| 115 | $htmlcontent =~ s{HREF="}{HREF="http://www.dsmz.de}igm; |
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| 116 | $htmlcontent =~ s{HREF=[^"]}{HREF=http://www.dsmz.de/}igm; ##" |
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| 117 | |
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| 118 | print OUTPUT $htmlcontent ; |
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| 119 | |
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| 120 | #exec ('netscape', $TMPOUT); |
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| 121 | print "file://" . $TMPOUT; |
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| 122 | |
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| 123 | ##print "$htmlcontent\n"; |
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