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revision 1.24, Wed Nov 17 14:40:19 2004 UTC revision 1.99, Tue Sep 19 21:19:14 2006 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use Tracer;
21    use FIG;
22  use Carp;  use Carp;
23  use Data::Dumper;  use Data::Dumper;
24  use LWP::UserAgent;  use LWP::UserAgent;
25  use LWP::Simple;  use LWP::Simple;
26    use URI::Escape;  # uri_escape()
27  use URI::URL;  use URI::URL;
28  use HTTP::Request::Common;  use HTTP::Request::Common;
29  use POSIX;  use POSIX;
30    
31  sub show_page {  use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
32      my($cgi,$html,$no_home) = @_;  my $raelib=new raelib;
33      my $i;  
34    
35    my $top_link_cache;
36    
37    
38    sub new
39    {
40        my($class) = @_;
41    
42        my $self = {};
43    
44        return bless $self, $class;
45    }
46    
47    sub top_link
48    {
49    
50      #      #
51      # Find the HTML header      # Determine if this is a toplevel cgi or one in one of the subdirs (currently
52        # just /p2p).
53      #      #
54    
55      my $html_hdr_file = "./Html/html.hdr";      return $top_link_cache if ($top_link_cache);
56    
57        my @parts = split(/\//, $ENV{SCRIPT_NAME});
58        my $top;
59        if ($parts[-2] eq 'FIG')
60        {
61            $top = '.';
62    #       warn "toplevel @parts\n";
63        }
64        elsif ($parts[-3] eq 'FIG')
65        {
66            $top = '..';
67    #       warn "subdir @parts\n";
68        }
69        else
70        {
71            $top = $FIG_Config::cgi_base;
72    #       warn "other @parts\n";
73        }
74    
75        $top_link_cache = $top;
76        return $top;
77    }
78    
79    sub compute_html_header
80    {
81        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
82        my($additional_insert, $user, %options ) = @_;
83    
84        local $/ = "\n";
85    
86        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
87        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
88    
89        my $html_hdr_file = "./Html/$header_name";
90      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
91      {      {
92          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
93      }      }
94        my @html_hdr = &FIG::file_read($html_hdr_file);
95    
96      my $html_tail_file = "./Html/html.tail";      # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
97      if (! -f $html_tail_file)  
98        #
99        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
100        # just /p2p).
101        #
102    
103        my @parts = split(/\//, $ENV{SCRIPT_NAME});
104        my $top;
105        if ($parts[-2] eq 'FIG')
106      {      {
107          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          $top = '.';
108    #       warn "toplevel @parts\n";
109        }
110        elsif ($parts[-3] eq 'FIG')
111        {
112            $top = '..';
113    #       warn "subdir @parts\n";
114        }
115        else
116        {
117            $top = $FIG_Config::cgi_base;
118    #       warn "other @parts\n";
119      }      }
120    
121      my @html_hdr = &FIG::file_read($html_hdr_file);      $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
     my $user = $cgi->param('user') || "";  
     push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );  
122    
123      if (@html_hdr)      if (@html_hdr)
124      {      {
125          my $insert_stuff;          my $insert_stuff;
126    
127            if (not $options{no_release_info})
128            {
129          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
130          my $ver = $ver[0];          my $ver = $ver[0];
131          chomp $ver;          chomp $ver;
# Line 46  Line 137 
137          }          }
138          my $host = &FIG::get_local_hostname();          my $host = &FIG::get_local_hostname();
139          $insert_stuff = "SEED version <b>$ver</b> on $host";          $insert_stuff = "SEED version <b>$ver</b> on $host";
140            }
141    
142            if ($additional_insert)
143            {
144                $insert_stuff .= "<br>" . $additional_insert;
145            }
146    
147          for $_ (@html_hdr)          for $_ (@html_hdr)
148          {          {
149              s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;              s,(href|img\s+src)="/FIG/,$1="$top/,g;
150                    s,(\?user\=)\",$1$user",;
151              if ($_ eq "<!-- HEADER_INSERT -->\n")              if ($_ eq "<!-- HEADER_INSERT -->\n")
152              {              {
153                  $_ = $insert_stuff;                  $_ = $insert_stuff;
# Line 57  Line 155 
155          }          }
156      }      }
157    
158        return @html_hdr;
159    }
160    
161      print $cgi->header;  sub show_page {
162        #warn "SHOWPAGE: cgi=", Dumper(@_);
163        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
164        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
165        my $i;
166    
167        my $top = top_link();
168    
169        # ARGUMENTS:
170        #     $cgi is the CGI method
171        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
172        #     $no_home eliminates ONLY the bottom FIG search link in a page
173        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
174        #     $css is a reference to a hash. The key is the name of the CSS sheet and the value is the URL of that sheet. Note the usual rules about relative css urls
175        #               the sheet named "Default" is considered to be the default style sheet, and if this is not set it points at $FIG_Config::HTML/css/default.css
176        #               the sheet named "Sans Serif" is considered to the the first alternate, and if this is not set it points at $FIG_Config::HTML/css/sanserif.css
177        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
178        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
179        #     $options is a reference to a hash of options that you can pass around the pages
180        #
181        # Find the HTML header
182        #
183    
184        my $html_tail_file = "./Html/$tail_name";
185        if (! -f $html_tail_file)
186        {
187            $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
188        }
189    
190        my $user = $cgi->param('user') || "";
191        my @html_hdr;
192        if ($alt_header && ref($alt_header) eq "ARRAY")
193        {
194           @html_hdr = @$alt_header;
195        }
196        else
197        {
198            @html_hdr = compute_html_header(undef,$user,%$options);
199        }
200    
201        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
202        # This modification adds the cookies if necessary
203    
204        # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
205        # to add cookies back in replace these two header lines with each other
206    
207        #print $cgi->header(-cookie=>$cookie);
208        print $cgi->header();
209    
210      #      #
211      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 76  Line 223 
223                       meta     => 1,                       meta     => 1,
224                       nextid   => 1,                       nextid   => 1,
225                       style    => 1,                       style    => 1,
226                       title    => 1                       title    => 1,
227                     );                     );
228    
229      #      #
# Line 119  Line 266 
266          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
267          {          {
268              $body_line = $i;              $body_line = $i;
269              $last;              last;
270          }          }
271    
272          #  Now the general case.          #  Now the general case.
# Line 175  Line 322 
322      #      #
323      #  <BODY> goes after last head line      #  <BODY> goes after last head line
324      #      #
325      #  RAE: Added the javascript for the buttons immediately after body.      #  RAE:
326        #  Added the javascript for the buttons immediately after body.
327      #  Note if no buttons are added we still (at the moment) add the script,      #  Note if no buttons are added we still (at the moment) add the script,
328      #  but it only adds a little text (495 characters) to the html and noone will notice!      #  but it only adds a little text (495 characters) to the html and noone will notice!
329        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
330    
331      if ( $body_line < 0 )      if ( $body_line < 0 )
332      {      {
         my $js=&javascript;  
333          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
334          splice( @$html, $body_line, 0, "<BODY>\n$js\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
335      }      }
336    
337      #      #
# Line 205  Line 353 
353          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
354      }      }
355    
356        # RAE:
357        # Add css here
358        # Note that at the moment I define these two sheets here. I think this should
359        # be moved out, but I want to try it and see what happens.  css has the format:
360        #
361        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
362    
363        # convert the default key to the right case. and eliminate dups
364        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
365    
366        if (!$css || !$css->{'Default'})
367        {
368           $css->{'Default'} = "Html/css/default.css";
369        }
370        if (!$css->{"Sans Serif"})
371        {
372           $css->{'Sans Serif'} = "Html/css/sanserif.css";
373        }
374    
375        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
376        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
377    
378        foreach my $k (keys %$css)
379        {
380           next if (lc($k) eq "default" || lc($k) eq "sans serif");
381           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
382        }
383    
384        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
385    
386        # RAE: also added support for external javascripts here.
387        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
388        # this solution allows us to source other files
389    
390        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
391        # it will reduce our overhead.
392    
393        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
394        push @$javasrc, "Html/css/FIG.js";
395        foreach my $script (@$javasrc) {
396            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
397        }
398    
399    
400    
401        splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.
402    
403      #      #
404      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
405      #      #
# Line 230  Line 425 
425  #       }  #       }
426    
427          $base_line = $head_end_line;          $base_line = $head_end_line;
428          splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );          #
429            # RDO 2005-1006. Remove this so proxying works better.
430            #
431    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
432      }      }
433    
434      #      #
# Line 280  Line 478 
478      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
479      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
480      #      #
   
481      my @tags = ();      my @tags = ();
482        # Check for a tracing queue.
483        my $traceString = QTrace("HTML");
484        if ($traceString) {
485            push @tags, $traceString;
486        }
487      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
488      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
489      {      {
# Line 304  Line 505 
505          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
506      }      }
507    
508      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
509        # and then we can join  with a "\n". This is because somethings put newlines in,
510        # and others don't. This should make nicer looking html
511        #
512        # chomp(@$html);
513        # print join "\n", @$html;
514        #
515        # Apparently the above still breaks things. This is the correct code:
516    
517        foreach $_ (@$html)
518        {
519            print $_;
520        }
521    
522  }  }
523    
524    
525    =head1 make_table
526    
527    The main method to convert an array into a table.
528    
529    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
530    
531    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
532    
533    =cut
534    
535  sub make_table {  sub make_table {
536      my($col_hdrs,$tab,$title, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
537      my(@tab);      my(@tab);
538    
539      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
540      push( @tab, "\n<table $border>\n",      my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;
541        my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;
542        push( @tab, "\n<table $border $width $class>\n",
543                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
544                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
545                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
546                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
547          );          );
548      my($i);      my($i);
549    
# Line 329  Line 556 
556              );              );
557      }      }
558      push(@tab,"</table>\n");      push(@tab,"</table>\n");
559    
560        # excelfile should be appropriate for a filename (no spaces/special characters)
561        if (defined $options{"excelfile"}) {push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
562    
563      return join("",@tab);      return join("",@tab);
564  }  }
565    
566    sub abstract_coupling_table {
567        my($cgi,$prot,$coupling) = @_;
568        my %fc;
569    
570        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
571        my $tab = [];
572        my %by_peg;
573        foreach my $x (@$coupling)
574        {
575            my($peg2,$psc,$type,$extra) = @$x;
576            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
577            {
578                if ($type =~  /^[ID]FC$/)
579                {
580                    $fc{$peg2} = 1;
581                }
582    
583                $by_peg{$peg2} += $psc;
584            }
585        }
586    
587        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
588                              or ($a->[0] cmp $b->[0])
589                              or ($b->[1] <=> $a->[1])
590                              or ($a->[2] cmp $b->[2]) } @$coupling)
591        {
592            my($peg2,$psc,$type,$extra) = @$x;
593            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
594        }
595    
596    
597         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
598    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
599    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
600    #    return @html;
601    
602        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
603    }
604    
605  sub expand {  sub expand {
606      my($x) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
607        my( $x, $tag ) = @_;
608    
609        $tag = "td" unless $tag;
610        my $endtag = $tag;
611    
612        # RAE modified this so that you can pass in a reference to an array where
613        # the first element is the data to display and the second element is optional
614        # things like colspan and align. Note that in this case you need to include the td
615        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
616    
617        # per GJO's request modified this line so it can take any tag.
618        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
619    
620      if ($x =~ /^\@([^:]+)\:(.*)$/)      if ($x =~ /^\@([^:]+)\:(.*)$/)
621      {      {
622          return "\t\t<td $1>$2</td>";          return "\t\t<$tag $1>$2</$endtag>";
623      }      }
624      else      else
625      {      {
626          return "\t\t<td>$x</td>";          return "\t\t<$tag>$x</$endtag>";
627      }      }
628  }  }
629    
630    
631    =head2 merge_table_rows()
632    
633    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
634    
635    Something like this:
636    
637        -----------------------
638        |    1     |    a     |
639        -----------------------
640        |    1     |    b     |
641        -----------------------
642        |    2     |    c     |
643        -----------------------
644        |    3     |    d     |
645        -----------------------
646        |    4     |    d     |
647        -----------------------
648        |    5     |    d     |
649        -----------------------
650    
651    Will become:
652    
653        -----------------------
654        |          |    a     |
655        |    1     |-----------
656        |          |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |          |
661        ------------          |
662        |    4     |    5     |
663        ------------          |
664        |    5     |          |
665        -----------------------
666    
667    
668    The method takes two arguments. The reference to the array that is the table ($tab). This is the standard table that is created for HTML.pm to draw, and a reference to a hash of columns that you don't want to merge together. The reference to the hash is optional, and if not included, everything will be merged.
669    
670     $tab=&HTML::merge_table_rows($tab);
671    
672     or
673    
674     $skip=(1=>1, 3=>1, 5=>1);
675     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
676    
677    
678    =cut
679    
680    
681    
682    
683    sub merge_table_rows {
684     # RAE:
685     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
686     # this block should merge adjacent rows that have the same text in them.
687     # use like this:
688     #      $tab=&HTML::merge_table_rows($tab);
689     # before you do a make_table call
690    
691     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
692     my ($tab, $skip)=@_;
693    
694     my $newtable;
695     my $lastrow;
696     my $rowspan;
697     my $refs;
698    
699     for (my $y=0; $y <= $#$tab; $y++) {
700     #$y is the row in the table;
701      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
702       # this is the user definable columns not to merge
703       if ($skip->{$x})
704       {
705        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
706        next;
707       }
708    
709       #$x is the column in the table
710       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
711       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
712    
713       # handle cells that are references to arrays
714       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
715    
716       # now we go back through the table looking where to draw the merge line:
717       my $lasty=$y;
718       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
719       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
720       if ($lasty == $y) {
721        # we always want to have something in rows that may otherwise be empty but should be there (see below)
722        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
723        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
724       }
725       else {$rowspan->[$lasty]->[$x]++}
726      }
727     }
728    
729     # now just join everything back together
730     for (my $y=0; $y <= $#$tab; $y++) {
731      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
732       if ($rowspan->[$y]->[$x]) {
733        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
734        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
735        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
736       }
737       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
738        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
739       }
740      }
741     }
742    
743    
744     # finally we have to remove any completely empty cells that have been added by the array mechanism
745     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
746     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
747     # I am sure that Gary can do this in one line, but I am hacking.
748     my @trimmed;
749     foreach my $a (@$newtable) {
750      my @row;
751      foreach my $b (@$a) {
752       push @row, $b if ($b);
753      }
754      push @trimmed, \@row;
755     }
756    
757     return \@trimmed;
758    }
759    
760    
761    
762    
763  sub set_ec_links {  sub set_ec_links {
764        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
765      my($cgi,$x) = @_;      my($cgi,$x) = @_;
766      my($before,$match,$after);      my($before,$match,$after);
767    
# Line 360  Line 776 
776  }  }
777    
778  sub ec_link {  sub ec_link {
779        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
780      my($role) = @_;      my($role) = @_;
781    
782      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 373  Line 790 
790  }  }
791    
792  sub role_link {  sub role_link {
793        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
794      my($cgi,$role) = @_;      my($cgi,$role) = @_;
795    
796      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 388  Line 806 
806  # text of the link.  # text of the link.
807  #  #
808  sub fid_link {  sub fid_link {
809        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
810      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url) = @_;
811      my($n);      my($n);
812    
813        my $top = top_link();
814    
815      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
816      {      {
817          if ($local)          if ($local)
# Line 408  Line 829 
829          {          {
830              $n = $fid;              $n = $fid;
831          }          }
832          if ($1 ne "peg") { return $n }  
833            my $link;
834            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
835            #added to format prophage and path island links to feature.cgi
836            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
837            if ($1 ne "peg" && ! $sprout)
838            {
839               my $user = $cgi->param('user');
840               if (! $user) { $user = "" }
841               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout";
842               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
843            }
844            else
845            {
846          my $user = $cgi->param('user');          my $user = $cgi->param('user');
847          if (! $user) { $user = "" }          if (! $user) { $user = "" }
848          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
849          my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
850          $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;  ###a
         #  
         # Elimin the p2p part if we're in that subdir. Ugh.  
         #  
         $link =~ s,p2p/protein.cgi,protein.cgi,;  
851    
852    ### This used to be
853    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
854    ###
855    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
856    ###
857    ### RAO
858    
859                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
860                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
861                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";
862                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
863            }
864          if ($just_url)          if ($just_url)
865          {          {
866              return $link;              return $link;
867          }          }
868          else          else
869          {          {
870              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
871          }          }
872      }      }
873      return $fid;      return $fid;
874  }  }
875    
876  sub family_link {  sub family_link {
877        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
878      my($family,$user) = @_;      my($family,$user) = @_;
879    
880      return $family;      return $family;
881  }  }
882    
 use URI::Escape;  
883    
884  sub get_html {  sub get_html {
885        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
886      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
887      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
888    
889      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
890      $ua->timeout( 900 );      $ua->timeout( 900 );
   
891      if ($type =~/post/i)      if ($type =~/post/i)
892      {      {
893          $args = [];          $args = [];
# Line 457  Line 899 
899          my $response = $ua->request($request);          my $response = $ua->request($request);
900          $out = $response->content;          $out = $response->content;
901      }      }
902      else  
903        if ($type =~/get/i)
904      {      {
905          @args = ();          @args = ();
906          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 505  Line 948 
948  }  }
949    
950  sub trim_output {  sub trim_output {
951        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
952      my($out) = @_;      my($out) = @_;
953      my $i;      my $i;
954    
# Line 542  Line 986 
986  }  }
987    
988  sub set_prot_links {  sub set_prot_links {
989        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
990      my($cgi,$x) = @_;      my($cgi,$x) = @_;
991      my($before,$match,$after);      my($before,$match,$after);
992    
# Line 552  Line 997 
997          $after = $3;          $after = $3;
998          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
999      }      }
1000      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1001      {      {
1002          $before = $1;          $before = $1;
1003          $match = $2;          $match = $2;
# Line 566  Line 1011 
1011          $after = $3;          $after = $3;
1012          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1013      }      }
1014        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1015        {
1016            $before = $1;
1017            $match = $2;
1018            $after = $3;
1019            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1020        }
1021        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1022        {
1023            $before = $1;
1024            $match = $2;
1025            $after = $3;
1026            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1027        }
1028    
1029        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1030        {
1031            $before = $1;
1032            $match = $2;
1033            $after = $3;
1034            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1035        }
1036    
1037        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1038        {
1039            $before = $1;
1040            $match = $2;
1041            $after = $3;
1042            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1043        }
1044    
1045        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1046        {
1047            $before = $1;
1048            $match = $2;
1049            $after = $3;
1050            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1051        }
1052    
1053        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1054        {
1055            $before = $1;
1056            $match = $2;
1057            $after = $3;
1058            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1059        }
1060    
1061        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1062        {
1063            $before = $1;
1064            $match = $2;
1065            $after = $3;
1066            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1067        }
1068      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1069      {      {
1070          $before = $1;          $before = $1;
# Line 594  Line 1093 
1093          $after = $3;          $after = $3;
1094          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1095      }      }
1096        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1097        {
1098            $before = $1;
1099            $match = $2;
1100            $after = $3;
1101            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1102        }
1103        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1104        {
1105            $before = $1;
1106            $match = $2;
1107            $after = $3;
1108            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1109        }
1110        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1111        {
1112            $before = $1;
1113            $match = $2;
1114            $after = $3;
1115            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1116        }
1117        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1118        {
1119            $before = $1;
1120            $match = $2;
1121            $after = $3;
1122            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1123        }
1124        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1125        {
1126            $before = $1;
1127            $match = $2;
1128            $after = $3;
1129            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1130        }
1131    # IPI stopped working. turn off for now.
1132    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1133    #    {
1134    #        $before = $1;
1135    #        $match = $2;
1136    #        $after = $3;
1137    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1138    #    }
1139        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1140        {
1141            #wormbase
1142    
1143            $before = $1;
1144            $match = $2;
1145            $after = $3;
1146            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1147        }
1148        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1149        {
1150            #flybase
1151    
1152            $before = $1;
1153            $match = $2;
1154            $after = $3;
1155            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1156        }
1157        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1158        {
1159            #flybase
1160    
1161            $before = $1;
1162            $match = $2;
1163            $after = $3;
1164            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1165        }
1166        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1167        {
1168            #flybase
1169    
1170            $before = $1;
1171            $match = $2;
1172            $after = $3;
1173            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1174        }
1175        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1176        {
1177    
1178          $before = $1;
1179          $match = $2;
1180          $after = $3;
1181    
1182          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1183        }
1184      return $x;      return $x;
1185  }  }
1186    
1187    sub trembl_link {
1188        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1189        my($cgi,$id) = @_;
1190    
1191        if ($id =~ /^tr\|(.*)/) {
1192          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1193        } else {
1194          return "invalid call to trembl link";
1195        }
1196    }
1197    
1198  sub refseq_link {  sub refseq_link {
1199        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1200      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1201    
1202      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1203      {      {
1204          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1205        }
1206        elsif ($id =~ /^[NXYZA]M_/)
1207        {
1208            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1209      }      }
1210  }  }
1211    
1212  sub gi_link {  sub gi_link {
1213        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1214      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1215    
1216      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1217      {      {
1218          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1219      }      }
1220      return $gi;      return $gi;
1221  }  }
1222    
1223    sub tigr_link {
1224        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1225        my($cgi,$tigr) = @_;
1226    
1227        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1228        {
1229            my $id=$1.$2;
1230            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1231        }
1232        elsif ($tigr =~ /^tigr\|(\S+)$/)
1233        {
1234            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1235        }
1236        return $tigr;
1237    }
1238    
1239    sub eric_link {
1240        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1241        my($cgi,$eric) = @_;
1242    
1243        if ($eric =~ /^eric\|(\S+)/)
1244        {
1245            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1246        }
1247        return $eric;
1248    }
1249    
1250    sub bhb_link {
1251        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1252        my($cgi,$bhb) = @_;
1253    
1254        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1255    }
1256    
1257    sub apidb_link {
1258        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1259        my($cgi,$api) = @_;
1260    
1261        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1262        {
1263            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1264        }
1265        return $api;
1266    }
1267    
1268    sub patric_link {
1269        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1270        my($cgi,$patric) = @_;
1271    
1272        if ($patric =~ /patric\|(.*)/)
1273        {
1274            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1275        }
1276        return $patric;
1277    }
1278    
1279    sub vbrc_link {
1280        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1281        my($cgi,$vbrc) = @_;
1282    
1283        if ($vbrc =~ /vbrc\|(.*)/)
1284        {
1285            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1286        }
1287        return $vbrc;
1288    }
1289    
1290    sub vectorbase_link {
1291        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1292        my($cgi,$vec) = @_;
1293        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1294    }
1295    
1296    
1297  sub uni_link {  sub uni_link {
1298        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1299      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1300    
1301      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1302      {      {
1303          return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1304            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1305      }      }
1306      return $uni;      return $uni;
1307  }  }
1308    
1309  sub sp_link {  sub sp_link {
1310        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1311      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1312    
1313      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1314      {      {
1315          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1316      }      }
1317      return $sp;      return $sp;
1318  }  }
1319    
1320  sub pir_link {  sub pir_link {
1321        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1322      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1323    
1324      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1325      {      {
1326          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1327      }      }
1328      return $pir;      return $pir;
1329  }  }
1330    
1331  sub kegg_link {  sub kegg_link {
1332        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1333      my($cgi,$kegg) = @_;      my($cgi,$kegg) = @_;
1334    
1335      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1336      {      {
1337          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1338      }      }
1339      return $kegg;      return $kegg;
1340  }  }
1341    
1342    sub ensembl_link {
1343        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1344        my($cgi,$ensembl) = @_;
1345    
1346        if ($ensembl =~ /^(\S+):(\S+)$/)
1347        {
1348            my $what=$1;
1349            my $key=$2;
1350            my $idx="All";
1351            if ($what eq "EnsemblGene") { $idx = "Gene" }
1352            if ($what eq "EnsemblTranscript") { $idx = "All" }
1353            if ($what eq "EnsemblProtein") { $idx = "All" }
1354    
1355            #I really want to get right to the transcript and peptide pages, but
1356            #can't see how to do that without knowing the org name too, which
1357            #I don't know at this point. (ensembl org name, not real org name)
1358    
1359            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1360        }
1361        return $ensembl;
1362    }
1363    
1364    sub entrezgene_link {
1365        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1366        my($cgi,$entrezgene) = @_;
1367    
1368        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1369        {
1370            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1371        }
1372        return $entrezgene;
1373    }
1374    
1375    sub mim_link {
1376        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1377        my($cgi,$mim) = @_;
1378    
1379        if ($mim =~ /^MIM:(\S+)$/)
1380        {
1381            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1382        }
1383        return $mim;
1384    }
1385    
1386    sub hgnc_link {
1387        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1388        my($cgi,$hgnc) = @_;
1389    
1390        if ($hgnc =~ /^HGNC:(\S+)$/)
1391        {
1392            return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1393        }
1394        return $mim;
1395    }
1396    
1397    sub unigene_link {
1398        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1399        my($cgi,$unigene) = @_;
1400    
1401        if ($unigene =~ /^UniGene:(\S+)$/)
1402        {
1403            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1404        }
1405        return $unigene;
1406    }
1407    
1408    sub ipi_link {
1409        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1410        my($cgi,$ipi) = @_;
1411    
1412        if ($ipi =~ /^IPI:(\S+)$/)
1413        {
1414            return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1415        }
1416        return $ipi;
1417    }
1418    
1419    sub wp_link {
1420        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1421        my($cgi,$wp) = @_;
1422    
1423        #wormbase
1424    
1425        if ($wp =~ /^WP:(\S+)$/)
1426        {
1427            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1428        }
1429        return $wp;
1430    }
1431    
1432    sub fb_link {
1433        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1434        my($cgi,$fb) = @_;
1435    
1436        #flybase
1437    
1438        if ($fb =~ /^FB:(\S+)$/)
1439        {
1440            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1441        }
1442        return $fb;
1443    }
1444    
1445    sub fborf_link {
1446        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1447        my($cgi,$fb) = @_;
1448    
1449        #flybase
1450    
1451        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1452        {
1453            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1454        }
1455        return $fb;
1456    }
1457    
1458    sub sgd_link {
1459        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1460        my($cgi,$sgd) = @_;
1461    
1462        #yeast
1463    
1464        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1465        {
1466            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1467        }
1468        return $sgd;
1469    }
1470    
1471    
1472    
1473    
1474  sub set_map_links {  sub set_map_links {
1475        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1476      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1477      my($before,$match,$after);      my($before,$match,$after);
1478    
# Line 672  Line 1488 
1488      return $x;      return $x;
1489  }  }
1490    
1491    
1492    
1493  sub map_link {  sub map_link {
1494        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1495      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1496    
1497      $user = $cgi->param('user');      $user = $cgi->param('user');
1498      $user = $user ? $user : "";      $user = $user ? $user : "";
1499      $org = $org ? $org : "";      $org = $org ? $org : "";
1500      my $url = "$FIG_Config::cgi_url/show_kegg_map.cgi?user=$user&map=$map&org=$org";  
1501        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1502    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1503      my $link = "<a href=\"$url\">$map</a>";      my $link = "<a href=\"$url\">$map</a>";
1504      return $link;      return $link;
1505  }  }
1506    
 sub javascript {  
         #### MODIFIED BY RAE TO ADD JAVA SUPPORT FOR CHECK ALL/UNCHECK ALL  
         # This routine takes three arguments, $html, $form, and $button  
         # $html is the ref to the array with the html in it  
         # $form is the name of the form. This must be added whenever start_form is called  
         # by including a -name entry. This is only used for the javascript  
         # $button is the name of the button that should be checked/unchecked.  
         #  
         # At the moment this add's four buttons:  
         # Check all, check's all  
         # Check first half will check the first 50% of the entries  
         # Check second half will check the second 50% of the entries  
         # Uncheck all will remove the checks.  
   
         # Note that the other change is I added a -name=>'fig_checked' to the start_form  
         # field. The name is needed for the java script.  
         #  
   
           $java_script=<<EOF;  
   <SCRIPT LANGUAGE="JavaScript">  
   <!-- Begin  
   function checkAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = true ;  
   }  
   
   function checkFirst(field)  
   {  
    for (i = 0; i < field.length/2; i++)  
    field[i].checked = true;  
   }  
   
   function checkSecond(field)  
   {  
    for (i=Math.round(field.length/2); i < field.length; i++)  
    field[i].checked = true ;  
   }  
   
   function uncheckAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = false ;  
   }  
   //  End -->  
   </script>  
 EOF  
         return $java_script;  
 }  
   
1507  sub java_buttons {  sub java_buttons {
1508        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1509    ## ADDED BY RAE    ## ADDED BY RAE
1510    # Provides code to include check all/first half/second half/none for javascrspt    # Provides code to include check all/first half/second half/none for javascrspt
1511    # this takes two variables - the form name provided in start_form with the    # this takes two variables - the form name provided in start_form with the
# Line 749  Line 1521 
1521  }  }
1522    
1523  sub sub_link {  sub sub_link {
1524        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1525      my($cgi,$sub) = @_;      my($cgi,$sub) = @_;
1526      my($sub_link);      my($sub_link);
1527    
1528      my $user = $cgi->param('user');      my $user = $cgi->param('user');
1529        my $esc_sub = uri_escape( $sub );
1530        $sub =~ s/\_/ /g;
1531      if ($user)      if ($user)
1532      {      {
1533          $sub_link = "<a href=./subsys.cgi?ssa_name=$sub&request=show_ssa&user=$user>$sub</a>";          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1534      }      }
1535      else      else
1536      {      {
1537          $sub_link = $sub;          $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";
1538      }      }
1539      return $sub_link;      return $sub_link;
1540  }  }
1541    
1542  1  sub reaction_link {
1543        my($reaction) = @_;
1544        if ($reaction =~ /^(\*)?(R\d+)/)
1545        {
1546            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1547        }
1548        return $reaction;
1549    }
1550    
1551    
1552    sub html_for_assignments {
1553        my($fig,$user,$peg_sets) = @_;
1554        my $i;
1555    
1556        my @vals = ();
1557        my $set = 1;
1558        foreach $peg_set (@$peg_sets)
1559        {
1560            for ($i=0; ($i < @$peg_set); $i++)
1561            {
1562                $peg = $peg_set->[$i];
1563                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1564            }
1565            $set++;
1566        }
1567    
1568        $ENV{'REQUEST_METHOD'} = 'GET';
1569        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1570        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1571        $out =~ s/^.*?<form/<form/si;
1572        $out =~ s/^(.*)<table.*/$1/si;
1573        return $out;
1574    }
1575    
1576    =head1 rss_feed
1577    
1578    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1579            SEED.rss                - everything gets written here
1580            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1581            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1582    
1583    
1584    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1585    
1586    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1587    
1588    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1589    
1590    The has can have these keys:
1591    
1592    REQUIRED:
1593    title       : the title. This is usually what is seen by the user in the pull down menu
1594    description : a more complete description that is often seen is rss viewers but not always
1595    link        : link to the item that was added/edited
1596    All other keys are treated as optional RSS arguments and written to the file.
1597    
1598    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1599    
1600    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1601    
1602    
1603    =cut
1604    
1605    sub rss_feed {
1606     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1607     my ($files, $args)=@_;
1608    
1609     # how many entries to store in the file
1610     my $max_entries=50;
1611    
1612     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1613    
1614     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1615     # check for the directory and if not, make it
1616     mkdir $filepath unless (-d $filepath);
1617    
1618     # note that $info is a hash of references to hashes that are written out as headers in the file
1619     my $info=
1620     {
1621      "SEED.rss" =>
1622       {
1623            title           => "The SEED",
1624            description     => "Latest news from the SEED",
1625            link            => "Html/rss/SEED.rss",
1626       },
1627    
1628      "SEEDsubsystems.rss" =>
1629      {
1630            title           => "SEED Subsystems",
1631            description     => "Recently updated SEED subsystems",
1632            link            => "Html/rss/SEEDsubsystems.rss",
1633      },
1634    
1635      "SEEDsubsystems.rss" =>
1636      {
1637            title           => "SEED Genomes",
1638            description     => "Genomes recently added to the SEED",
1639            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1640      },
1641    
1642     };
1643    
1644    
1645     # build the new xml
1646     my $xml = "\t<item>\n";
1647     foreach my $qw ("title", "description", "link") {
1648      unless ($args->{$qw}) {
1649       print STDERR "You need to include a $qw tag in your RSS description\n";
1650       return(0);
1651      }
1652      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1653      # so we are going to pull out the links and uri_escape just the part after the .cgi
1654      if ($qw eq "link")
1655      {
1656       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1657       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1658      }
1659    
1660      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1661      delete $args->{$qw};
1662     }
1663    
1664     foreach my $tag (grep {!/type/i} keys %$args)
1665     {
1666      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1667     }
1668    
1669     $xml .= "\t</item>\n";
1670    
1671    
1672     my @files=("SEED.rss");
1673     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1674    
1675     foreach my $file ("SEED.rss", @$files)
1676     {
1677      if (-e "$filepath/$file")
1678      {
1679       my @out; # the new content of the file
1680       my $itemcount=0; # how many <item> </item>'s are we keeping
1681       my $initem; # are we in an item?
1682       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1683       while (<IN>)
1684       {
1685        if (/\<item\>/) {
1686         push @out, $xml, unless ($itemcount);
1687         $itemcount++;
1688         $initem=1;
1689        }
1690        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1691        next if ($initem && $itemcount > $max_entries);
1692        push @out, $_;
1693       }
1694       close IN;
1695       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1696       print OUT @out;
1697      }
1698      else
1699      {
1700       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1701       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1702       if ($info->{$file})
1703       {
1704         # we're going to sanity check each of the three options we output, just to be sure
1705         foreach my $qw ("title", "description", "link")
1706         {
1707           if ($info->{$file}->{$qw})
1708           {
1709              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1710           } else {
1711              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1712           }
1713         }
1714       }
1715       else {
1716        print STDERR "Please define title, link, and description information for $file\n";
1717        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1718       }
1719       print OUT "\n", $xml;
1720       print OUT "\n", "</channel>\n</rss>\n"
1721      }
1722     }
1723    }
1724    
1725    
1726    
1727    1;
1728    

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