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1 : overbeek 1.1 # -*- perl -*-
2 :     #
3 : golsen 1.7 # Copyright (c) 2003-2008 University of Chicago and Fellowship
4 : overbeek 1.1 # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 : golsen 1.8 #
20 :     # DBMS tables used:
21 :     #
22 : golsen 1.11 # dlits
23 : golsen 1.8 # flds => "status char(1), md5_hash varchar(32), pubmed varchar(16), curator varchar(30), go_code varchar(15)"
24 :     #
25 :     # titles
26 :     # flds => "pubmed varchar(16), title varchar(1000)"
27 :     #
28 :     # hash_role
29 :     # flds => "md5_hash char(32), role varchar(1000)"
30 :     #
31 :     # curr_role
32 :     # flds => "curator varchar(30), role varchar(1000)"
33 :     #
34 :     # genome_hash
35 :     # flds => "genome varchar(32), md5_hash char(32)"
36 :     #
37 : overbeek 1.1
38 :     use FIG;
39 :     my $fig = new FIG;
40 :    
41 :     use HTML;
42 :     use strict;
43 :    
44 :     use CGI;
45 :     my $cgi = new CGI;
46 :    
47 : golsen 1.11 use Data::Dumper;
48 : overbeek 1.1
49 :     if (0)
50 :     {
51 :     my $VAR1;
52 :     eval(join("",`cat /tmp/get_dlit_parms`));
53 :     $cgi = $VAR1;
54 :     # print STDERR &Dumper($cgi);
55 :     }
56 :    
57 :     if (0)
58 :     {
59 :     print $cgi->header;
60 :     my @params = $cgi->param;
61 :     print "<pre>\n";
62 :     foreach $_ (@params)
63 :     {
64 : golsen 1.7 print "$_\t:",join(",",$cgi->param($_)),":\n";
65 : overbeek 1.1 }
66 :    
67 :     if (0)
68 :     {
69 : golsen 1.7 if (open(TMP,">/tmp/get_dlit_parms"))
70 :     {
71 :     print TMP &Dumper($cgi);
72 :     close(TMP);
73 :     }
74 : overbeek 1.1 }
75 :     exit;
76 :     }
77 :     my($genome);
78 :    
79 :     my $html = [];
80 : golsen 1.11 push @$html, "<TITLE>Get Dlits</TITLE>\n";
81 : overbeek 1.1
82 : golsen 1.7 my $user = $cgi->param('user'); # Current user
83 :     my $curator = $cgi->param('curator') || ''; # Filter roles by subsystem curator
84 :     my $genomeD = $cgi->param('genomeD'); # Find lit by genome
85 : golsen 1.8 my $ref_id = $cgi->param('ref_id'); # Show data by reference
86 : golsen 1.7 my $role = $cgi->param('role'); # Find lit by role
87 :     my $show_just = $cgi->param('show_just'); # Filter lit by status
88 : overbeek 1.1 $show_just = ($show_just eq "all") ? '' : $show_just;
89 :    
90 : golsen 1.7 # Requested actions:
91 :    
92 :     my ( $submit1, $submit2, $submit3, $submit4, $submit5 );
93 :     if ( $cgi->param( 'Process Changes' ) ) { $submit5 = 1 }
94 : golsen 1.8 if ( $ref_id ) {}
95 :     elsif ( $cgi->param( 'Change subsystem curator' ) ) {}
96 : golsen 1.7 elsif ( $cgi->param( 'Show Genomes' ) ) { $submit1 = 1 }
97 :     elsif ( $cgi->param( 'Show Roles' ) ) { $submit2 = 1 }
98 :     elsif ( $cgi->param( 'Show Genome' ) ) { $submit3 = 1 }
99 :     elsif ( $cgi->param( 'Show Role' ) ) { $submit4 = 1 }
100 :    
101 :     my $done = 0;
102 :    
103 : overbeek 1.1 my $rdbH = $fig->db_handle;
104 :    
105 : golsen 1.7 if (! -d "$FIG_Config::data/Dlits")
106 : overbeek 1.1 {
107 : golsen 1.7 push( @$html, $cgi->h1("dlit data are not installed") );
108 :     $done = 1;
109 : overbeek 1.1 }
110 : golsen 1.7 elsif ( ! $user )
111 : overbeek 1.1 {
112 : golsen 1.7 push( @$html, $cgi->h2('To curate literature, please provide a user name') );
113 :     push( @$html, $cgi->start_form(-action => "get_dlits.cgi", -method => 'post'),
114 :     'Username: ',
115 :     $cgi->textfield( -name=>"user", -size => 20 ),
116 :     $cgi->br,
117 :     $cgi->submit( 'Set user' ),
118 :     $cgi->end_form
119 :     );
120 :     $done = 1;
121 : overbeek 1.1 }
122 : golsen 1.7
123 : golsen 1.11
124 :     # This is a one-time special case to add an index to the dlits table
125 :    
126 :     if ( $user eq 'master:gjo' && $cgi->param('add_pubmed_index') ) { &add_pubmed_index( $rdbH, $html ) }
127 :    
128 :    
129 : golsen 1.7 # Process a page of curated literature ----------------------------------------
130 :    
131 :     if ( $submit5 && ! $done )
132 :     {
133 :     &process_changes( $fig, $cgi, $html );
134 :     my $prev_req = $cgi->param( 'prev_req' );
135 :     $submit3 = 1 if $prev_req eq 'Show Genome';
136 :     $submit4 = 1 if $prev_req eq 'Show Role';
137 : overbeek 1.1 }
138 : golsen 1.7
139 :     # If there is a problem, skip the rest of the action tests --------------------
140 :     # This is organized this way so that a useful page can be
141 :     # provided after processing a curated page.
142 :    
143 :     if ( $done ) { }
144 :    
145 : golsen 1.8 # All sequences in a reference ------------------------------------------------
146 :    
147 :     elsif ( $ref_id )
148 :     {
149 :     my $and_status = $show_just ? " AND ( dlits.status = '$show_just' )" : '';
150 : golsen 1.11 my $tuples = $rdbH->SQL( "SELECT DISTINCT status,md5_hash,curator "
151 :     . "FROM dlits "
152 :     . "WHERE ( pubmed = '$ref_id' )"
153 :     . $and_status
154 : golsen 1.8 );
155 :     my @to_display = ();
156 :     foreach my $x ( @$tuples )
157 :     {
158 : golsen 1.10 my( $status, $hash, $prev_curator ) = @$x;
159 :     my @pegs = grep { $fig->is_real_feature($_) }
160 :     $fig->pegs_with_md5( $hash );
161 : golsen 1.8 if ( @pegs > 0 )
162 :     {
163 : golsen 1.10 push( @to_display, [ $status, $pegs[0], $ref_id, $prev_curator ] );
164 : golsen 1.8 }
165 :     }
166 :    
167 :     &display_set( $fig, $cgi, $html, \@to_display, "Genes linked to Reference: $ref_id", 'Show Reference' ) ;
168 :     }
169 :    
170 : golsen 1.7 # Literature selected by role -------------------------------------------------
171 :    
172 :     elsif ( $submit4 && $role )
173 : overbeek 1.1 {
174 : golsen 1.7 my $roleQ = quotemeta $role;
175 : golsen 1.8 my $and_status = $show_just ? " AND ( dlits.status = '$show_just' )" : '';
176 : golsen 1.11 my $tuples = $rdbH->SQL( "SELECT DISTINCT dlits.status,dlits.md5_hash,dlits.pubmed,dlits.curator "
177 :     . "FROM hash_role,dlits "
178 :     . "WHERE ( hash_role.role = '$roleQ') AND ( hash_role.md5_hash = dlits.md5_hash )"
179 : golsen 1.8 . $and_status
180 : golsen 1.7 );
181 : overbeek 1.1 my @to_display = ();
182 : golsen 1.8 foreach my $x ( @$tuples )
183 : overbeek 1.1 {
184 : golsen 1.10 my( $status, $hash, $pubmed, $prev_curator ) = @$x;
185 :     my @pegs = grep { $fig->is_real_feature($_) }
186 :     $fig->pegs_with_md5( $hash );
187 : golsen 1.8 if ( @pegs > 0 )
188 : golsen 1.7 {
189 : golsen 1.10 push( @to_display, [ $status, $pegs[0], $pubmed, $prev_curator ] );
190 : golsen 1.7 }
191 : overbeek 1.1 }
192 : golsen 1.8
193 :     &display_set( $fig, $cgi, $html, \@to_display, "Genes for Role: $role", 'Show Role' );
194 : golsen 1.7 }
195 :    
196 :     # Show the role list ----------------------------------------------------------
197 :    
198 :     elsif ( $submit2 || $submit4 )
199 :     {
200 :     # Did user request role literature, and not select a role?
201 :     push @$html, $cgi->h3( '<FONT Color=red>Please select a role.</FONT>' ) if $submit4;
202 :    
203 :     my $where1 = $show_just ? " AND (dlits.status = '$show_just')" : "";
204 :     my $where2 = $curator ? " AND (curr_role.curator = '$curator' AND curr_role.role = hash_role.role)" : "";
205 :    
206 :     my @roles = sort { lc $a cmp lc $b } # Make sort case insensitive
207 :     map { $_->[0] }
208 : golsen 1.11 @{ $rdbH->SQL( "SELECT DISTINCT hash_role.role "
209 :     . "FROM hash_role,dlits,curr_role "
210 :     . "WHERE hash_role.md5_hash = dlits.md5_hash $where1 $where2"
211 : golsen 1.7 ) };
212 :     push( @$html, $cgi->start_form(-action => "get_dlits.cgi", -method => 'post'),
213 : golsen 1.9 $cgi->hidden( -name => 'user', -value => $user ),
214 : golsen 1.10 $cgi->hidden( -name => 'curator', -value => $curator )
215 : golsen 1.7 );
216 :    
217 :     my $whom = $curator ? "'$curator'" : "any one";
218 :     my $status = $show_just ? " with literature of status code '$show_just':" : ":";
219 :     push( @$html, $cgi->h3( "Subsystem roles curated by $whom" . $status ) );
220 :    
221 :     push( @$html, $cgi->scrolling_list( -name => 'role',
222 :     -values => [@roles],
223 :     -size => 30
224 :     ),
225 :     $cgi->br, &show_just_selector( $cgi ),
226 :     $cgi->br, $cgi->submit( 'Show Role' ),
227 :     $cgi->br, $cgi->submit( 'Show Genomes' ),
228 :     $cgi->br, $cgi->submit( 'Change subsystem curator' ), " currently '$curator'.",
229 :     $cgi->end_form
230 :     );
231 : overbeek 1.1 }
232 : golsen 1.7
233 :     # Literature selected by genome -----------------------------------------------
234 :    
235 :     elsif ( $submit3 && $genomeD && ( $genomeD =~ /\((\d+\.\d+)\)$/ ) )
236 : overbeek 1.1 {
237 : golsen 1.7 my $genome = $1;
238 :     my $where = $show_just ? " AND (dlits.status = '$show_just')" : '';
239 : golsen 1.11 my $tuples = $rdbH->SQL( "SELECT DISTINCT dlits.status,dlits.md5_hash,dlits.pubmed,dlits.curator "
240 :     . "FROM genome_hash,dlits "
241 :     . "WHERE genome_hash.genome = '$genome' AND genome_hash.md5_hash = dlits.md5_hash $where"
242 : golsen 1.7 );
243 : overbeek 1.1 my @to_display = ();
244 : golsen 1.7 foreach my $x ( @$tuples )
245 : overbeek 1.1 {
246 : golsen 1.10 my ( $status, $hash, $pubmed, $prev_curator ) = @$x;
247 :     push @to_display, map { [ $status, $_, $pubmed, $prev_curator ] }
248 :     grep { &FIG::genome_of($_) eq $genome && $fig->is_real_feature($_) }
249 :     $fig->pegs_with_md5($hash);
250 : overbeek 1.1 }
251 : golsen 1.10
252 : golsen 1.7 &display_set( $fig, $cgi, $html, \@to_display, "Genes for $genomeD", 'Show Genome' );
253 :     }
254 :    
255 :     # Show genome list ------------------------------------------------------------
256 :    
257 :     elsif ( $submit1 || $submit3 )
258 :     {
259 :     # Did user request genome literature, and not select a genome?
260 :     push @$html, $cgi->h3( '<FONT Color=red>Please select a genome.</FONT>' ) if $submit3;
261 :    
262 :     my $where = $show_just ? " AND (dlits.status = '$show_just')" : "";
263 :    
264 : golsen 1.11 my $genomes = $rdbH->SQL( "SELECT DISTINCT genome_hash.genome "
265 :     . "FROM genome_hash,dlits "
266 :     . "WHERE genome_hash.md5_hash = dlits.md5_hash $where"
267 : golsen 1.7 );
268 :     my @genomes = sort { lc $a cmp lc $b } # Make sort case insensitive
269 :     map { &compute_genome_label( $fig, $_->[0] ) }
270 :     @$genomes;
271 :    
272 :     push( @$html, $cgi->start_form(-action => "get_dlits.cgi", -method => 'post'),
273 : golsen 1.9 $cgi->hidden( -name => 'user', -value => $user ),
274 :     $cgi->hidden( -name => 'curator', -value => $curator ),
275 : golsen 1.7 $cgi->scrolling_list( -name => 'genomeD',
276 :     -values => [@genomes],
277 :     -size => 30
278 :     ),
279 :     $cgi->br, &show_just_selector( $cgi ),
280 : golsen 1.11 $cgi->br, $cgi->submit( 'Show Genome' ), ' selected above.',
281 : golsen 1.7 $cgi->br, $cgi->submit( 'Show Roles' ),
282 : golsen 1.11 ( $curator ? " for subsystem curator '$curator'." : '' ),
283 : golsen 1.7 $cgi->br, $cgi->submit( 'Change subsystem curator' ), " currently '$curator'.",
284 :     $cgi->end_form
285 :     );
286 : overbeek 1.1 }
287 : golsen 1.7
288 :     # Default = display subsystem curators ----------------------------------------
289 :    
290 : overbeek 1.1 else
291 :     {
292 : golsen 1.7 my @cur = map { $_->[0] }
293 :     sort { $a->[1] cmp $b->[1] || length $a->[0] <=> length $b->[0] }
294 :     map { my $cur = $_->[0];
295 :     my $nam = lc $cur;
296 :     $nam =~ s/^master[:_]?//;
297 :     [ $cur, $nam ]
298 :     }
299 :     @{ $rdbH->SQL( "SELECT DISTINCT curator FROM dlits" ) };
300 :     my $curN = @cur;
301 :    
302 :     push( @$html, $cgi->start_form(-action => "get_dlits.cgi", -method => 'post'),
303 : golsen 1.9 $cgi->hidden( -name => 'user', -value => $user ),
304 : golsen 1.7 $cgi->scrolling_list( -name => 'curator',
305 :     -values => [ @cur ],
306 :     -size => $curN
307 :     ),
308 :     $cgi->br,
309 :     &show_just_selector( $cgi ),
310 :     $cgi->submit( 'Show Roles' ),
311 :     $cgi->br,
312 :     $cgi->submit( 'Show Genomes' ),
313 :     $cgi->end_form
314 :     );
315 :     }
316 :     &HTML::show_page($cgi,$html);
317 :     exit;
318 : overbeek 1.1
319 :    
320 : golsen 1.7 sub show_just_selector
321 :     {
322 :     my ( $cgi, $html ) = @_;
323 :     my $default = $cgi->param( 'show_just' );
324 :     $default =~ /^[ A-Z]$/ or $default = 'all';
325 :     return 'Show literature links with all status codes, or pick a specific one: '
326 :     . $cgi->scrolling_list( -name => 'show_just',
327 :     -values => ['all',' ','D','R','N','G'],
328 :     -default => $default,
329 :     -override => 1,
330 :     -size => 1
331 :     )
332 :     . $cgi->br;
333 : overbeek 1.1 }
334 :    
335 :    
336 :     sub compute_genome_label
337 :     {
338 :     my($fig, $org) = @_;
339 :    
340 :     my $gs = $fig->genus_species($org);
341 :     return "$gs ($org)";
342 :     }
343 :    
344 : golsen 1.7
345 : overbeek 1.1 sub title_of {
346 : golsen 1.8 my( $fig, $pubmed ) = @_;
347 : overbeek 1.1
348 :     my $rdbH = $fig->db_handle;
349 : golsen 1.11 my $retval = $rdbH->SQL( "SELECT title "
350 :     . "FROM pubmed_titles "
351 :     . "WHERE (pubmed = $pubmed)"
352 : golsen 1.7 );
353 :     return ( @$retval > 0 ) ? $retval->[0]->[0] : "";
354 :     }
355 :    
356 :    
357 :     sub pubmed_link
358 :     {
359 :     return "<a target=_blank href=http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=$_[0]>$_[0]</a>";
360 : overbeek 1.1 }
361 : golsen 1.7
362 : overbeek 1.1
363 :     sub display_set {
364 : golsen 1.7 my( $fig, $cgi, $html, $to_display, $tab_title, $submit ) = @_;
365 : overbeek 1.1
366 : golsen 1.7 my %status_code = ( 'D' => 1, ' ' => 2, 'N' => 3, 'R' => 4, 'G' => 5 );
367 : overbeek 1.1
368 : golsen 1.7 # @$to_distplay items are [ $status, $peg, $pubmed ]
369 : overbeek 1.1
370 : golsen 1.7 foreach $_ ( @$to_display ) { $_->[0] =~ s/^\s*$/ /; } # fix empty status strings
371 :     my @tuples = sort { ( $status_code{$a->[0]} <=> $status_code{$b->[0]} )
372 :     or &FIG::by_fig_id( $a->[1], $b->[1] )
373 : golsen 1.10 or ( $a->[2] <=> $b->[2] ) # Numeric sort of PMID
374 : golsen 1.7 }
375 :     @$to_display;
376 : overbeek 1.1 my $total_tuples = @tuples;
377 :    
378 : golsen 1.7 my $from; # Offset to first item displayed
379 : golsen 1.8 my $n_per_page = 100; # Really the lines per page
380 : golsen 1.7
381 :     if ( $cgi->param( 'Go to item numbers' ) )
382 :     {
383 :     $from = $cgi->param( 'offset_select' );
384 :     }
385 :     else
386 :     {
387 :     $from = $cgi->param( 'from_line' ) || 0;
388 : golsen 1.8 $from -= $n_per_page if $cgi->param( 'Previous page' );
389 :     $from += $n_per_page if $cgi->param( 'Next page' );
390 : golsen 1.7 }
391 :    
392 :     # Cut down the array to that to be displayed
393 :    
394 :     if ( $total_tuples > 0 )
395 :     {
396 :     if ( $from < 0 ) { $from = 0 }
397 :     if ( $from > $total_tuples )
398 :     {
399 : golsen 1.8 $from = $n_per_page * int( ( $total_tuples - 1 ) / $n_per_page );
400 : golsen 1.7 }
401 :     splice( @tuples, 0, $from );
402 : golsen 1.8 splice( @tuples, $n_per_page );
403 : golsen 1.7 }
404 : overbeek 1.1 else
405 :     {
406 : golsen 1.7 undef $from;
407 : overbeek 1.1 }
408 :    
409 : golsen 1.7 # Add status code key at top of page
410 :    
411 :     &desc( $html );
412 :    
413 :     # Build the html form
414 :    
415 :     push( @$html, $cgi->start_form(-action => "get_dlits.cgi", -method => 'post') );
416 :    
417 :     # Current user
418 :     my $user = $cgi->param('user');
419 :     push( @$html, $cgi->hidden( -name => 'user', -value => $user, -override => 1 ) );
420 :    
421 :     # Filter roles by subsystem curator
422 : golsen 1.8 my $curator = $cgi->param('curator');
423 : golsen 1.7 push( @$html, $cgi->hidden( -name => 'curator', -value => $curator, -override => 1 ) ) if $curator;
424 :    
425 :     # Find lit by genome
426 :     my $genomeD = $cgi->param('genomeD');
427 :     push( @$html, $cgi->hidden( -name => 'genomeD', -value => $genomeD, -override => 1 ) ) if $genomeD;
428 :    
429 : golsen 1.8 # Show sequences associated with a reference
430 :     my $ref_id = $cgi->param('ref_id');
431 :     push( @$html, $cgi->hidden( -name => 'ref_id', -value => $ref_id, -override => 1 ) ) if $ref_id;
432 :    
433 : golsen 1.7 # Find lit by role
434 :     my $role = $cgi->param('role');
435 :     push( @$html, $cgi->hidden( -name => 'role', -value => $role, -override => 1 ) ) if $role;
436 :    
437 :     # Requested action
438 :     push( @$html, $cgi->hidden( -name => 'prev_req', -value => $submit, -override => 1 ) ) if $submit;
439 :    
440 :     # Used to inherit action
441 :     push( @$html, $cgi->hidden( -name => $submit, -value => 1, -override => 1 ) ) if $submit;
442 :    
443 :     push( @$html, $cgi->br );
444 :    
445 : golsen 1.8 # If this is not a table built around one reference, we want to append
446 :     # links to all proteins associated with the reference. We will
447 :     # compute this on a unique set of the references:
448 :    
449 :     my %genes_in_pub;
450 :     if ( ! $ref_id )
451 :     {
452 :     foreach ( @tuples )
453 :     {
454 :     my $pub = $_->[2];
455 :     next if defined $genes_in_pub{ $pub };
456 :     # This count intentionally omits filtering by status
457 :     $genes_in_pub{ $pub } = scalar ( &all_seqs_in_pub( $fig, $pub ) );
458 :     }
459 :     }
460 :    
461 : golsen 1.7 # Build the status selection table
462 :    
463 : golsen 1.10 my $col_hdrs = [' ','G','N','R','D','Curator','PEG','Function','Genus/Species','PubMed','Title'];
464 : golsen 1.7 my $tab = [];
465 : overbeek 1.1 my $i;
466 : golsen 1.8 for ( $i = 0; ($i < @tuples); $i++ )
467 : overbeek 1.1 {
468 : golsen 1.7 my $tuple = $tuples[$i];
469 : golsen 1.10 my( $status, $peg, $pubmed, $prev_curator ) = @$tuple;
470 :     next if ( ! $fig->is_real_feature($peg) ); # This should never fail
471 :    
472 :     $prev_curator =~ s/^master://i; # Remove master from displayed curator
473 : golsen 1.7 my $gs = $fig->genus_species( &FIG::genome_of( $peg ) );
474 :     $gs =~ s/^(\S+\s+\S+).*$/$1/;
475 :     my $title = &title_of( $fig, $pubmed );
476 :     my $func = $fig->function_of($peg);
477 :     my @codes = $cgi->radio_group( -name => "tuple:$peg:$pubmed:$status",
478 :     -values => [' ','G','N','R','D'],
479 :     -default => "$status",
480 :     -nolabels => 1
481 :     );
482 :    
483 : golsen 1.8 my $pub_link = &pubmed_link( $pubmed );
484 :    
485 :     # Does this paper cover more than one protein?
486 :    
487 :     if ( $genes_in_pub{ $pubmed } > 1 )
488 :     {
489 : golsen 1.11 # This link intentionally omits $show_just
490 : golsen 1.9 my $href = "get_dlits.cgi?user=$user&ref_id=$pubmed";
491 :     $pub_link .= "<BR />(<A HRef='$href' Target=_blank>$genes_in_pub{$pubmed} seqs</A>)";
492 : golsen 1.8 }
493 : golsen 1.11 if ( $i && ($i % 15) == 0 ) { push(@$tab,$col_hdrs) }
494 : golsen 1.10 push( @$tab, [ @codes, $prev_curator, &HTML::fid_link( $cgi, $peg ), $func, $gs, $pub_link, $title ] );
495 : golsen 1.7 }
496 :    
497 :     push( @$html,&HTML::make_table( $col_hdrs, $tab, $tab_title ) );
498 :    
499 :     push( @$html, $cgi->br, &show_just_selector( $cgi ) );
500 :    
501 :     # Navigation controls through long lists
502 :    
503 : golsen 1.8 if ( defined( $from ) && ( $total_tuples > $n_per_page ) )
504 : golsen 1.7 {
505 :     my $i1 = $from + 1;
506 : golsen 1.8 my $i2 = $from + $n_per_page;
507 : golsen 1.7 $i2 = $total_tuples if $i2 > $total_tuples;
508 :     push( @$html, $cgi->hidden( -name => 'from_line', -value => $from, -override => 1 ) );
509 :     push( @$html, $cgi->br, "Currently displaying items $i1 - $i2 of $total_tuples.", $cgi->br );
510 :     push( @$html, $cgi->submit( 'Previous page' ) ) if $from > 0;
511 :     push( @$html, $cgi->submit( 'Next page' ) ) if $i2 < $total_tuples;
512 :    
513 :     my @offsets;
514 :     my %labels;
515 : golsen 1.8 for ( my $i = 0; $i < $total_tuples; $i += $n_per_page )
516 : golsen 1.7 {
517 :     push @offsets, $i;
518 : golsen 1.8 my $imax = $i + $n_per_page;
519 : golsen 1.7 $imax = $total_tuples if $imax > $total_tuples;
520 :     $labels{ $i } = ( $i+1 ) . " - $imax";
521 :     }
522 :     push( @$html, $cgi->submit( 'Go to item numbers' ),
523 :     $cgi->scrolling_list( -name => 'offset_select',
524 :     -values => \@offsets,
525 :     -labels => \%labels,
526 :     -default => $from,
527 :     -size => 1,
528 :     -override => 1
529 :     ),
530 :     $cgi->br );
531 : overbeek 1.1 }
532 : golsen 1.7
533 :     # Some action buttons:
534 :    
535 :     push( @$html, $cgi->br, $cgi->submit( 'Process Changes' ), "entered on this page." );
536 :    
537 : golsen 1.8 # Display some general navigation buttons. However, these are not
538 :     # consistent with the intended use of the publication-based view.
539 : golsen 1.7
540 : golsen 1.8 if ( ! $ref_id )
541 : golsen 1.7 {
542 : golsen 1.8 push( @$html, $cgi->br, $cgi->submit( 'Show Genomes' ), "discarding any changes made on this page." );
543 :     if ( $curator )
544 :     {
545 :     push( @$html, $cgi->br, $cgi->submit( 'Show Roles' ),
546 :     "for subsystem curator '$curator', discarding any changes made on this page." );
547 :     }
548 :     push( @$html, $cgi->br, $cgi->submit( 'Change subsystem curator' ), " currently '$curator', discarding any changes made on this page." );
549 : golsen 1.7 }
550 :    
551 : golsen 1.8 push( @$html, $cgi->end_form );
552 :     }
553 :    
554 : golsen 1.7
555 : golsen 1.11 # dlits
556 : golsen 1.8 # flds => "status char(1), md5_hash varchar(32), pubmed varchar(16), curator varchar(30), go_code varchar(15)"
557 :    
558 :     sub all_seqs_in_pub {
559 :     my ( $fig, $pubmed, $status ) = @_;
560 :     my $rdbH = $fig->db_handle;
561 :     my $and_status = $status ? " AND ( status = '$status' )" : "";
562 : golsen 1.11 my $response = $rdbH->SQL( "SELECT DISTINCT md5_hash "
563 :     . "FROM dlits "
564 :     . "WHERE ( pubmed = '$pubmed' )"
565 :     . $and_status
566 : golsen 1.8 );
567 :     return ( ref $response ) ? map { $_->[0] } @$response : ();
568 : overbeek 1.1 }
569 :    
570 : golsen 1.7
571 : overbeek 1.4 sub desc {
572 : golsen 1.7 my( $html ) = @_;
573 : overbeek 1.4
574 : golsen 1.7 my $col_hdrs = [ "Code", "Meaning" ];
575 :     my $tab = [ [ [" ","TD Align=center"], "No one has curated this link yet" ],
576 :     [ ["G","TD Align=center"], "Genome paper - marks all uncurated protein links of this paper to 'G' (implicitly irrelevant)" ],
577 :     [ ["N","TD Align=center"], "Not relevant to this protein" ],
578 :     [ ["R","TD Align=center"], "Relevant, but not strong enough to determine function" ],
579 :     [ ["D","TD Align=center"], "Direct reference that can be used to support function assertion" ]
580 :     ];
581 :     push( @$html, &HTML::make_table( $col_hdrs, $tab, "Code Meanings" ), "<hr>" );
582 : overbeek 1.4 }
583 :    
584 : golsen 1.7
585 : overbeek 1.1 sub process_changes {
586 : golsen 1.7 my( $fig, $cgi, $html ) = @_;
587 :     my $user = $cgi->param('user');
588 : overbeek 1.1
589 :     my @tuples = grep { $_->[2] ne $_->[3] }
590 :     map { ($_ =~ /^tuple:(fig\|\d+\.\d+\.peg\.\d+)\s*:\s*(\d+)\s*:([ RDGN])/) ? [$1,$2,$3,$cgi->param($_)] : () }
591 :     $cgi->param();
592 : golsen 1.7 my $n_change = 0;
593 :     foreach my $tuple ( @tuples )
594 : overbeek 1.1 {
595 : golsen 1.7 my( $peg, $pubmed, $from, $to ) = @$tuple;
596 :     $fig->add_dlit( -status => $to,
597 :     -peg => $peg,
598 :     -pubmed => $pubmed,
599 :     -curator => $user,
600 :     -override => 1
601 :     );
602 :     $n_change++;
603 : overbeek 1.1 }
604 : golsen 1.7
605 :     push( @$html, $cgi->h2( "<FONT Color=green>Made $n_change requested changes.</FONT>" ) );
606 : overbeek 1.1 }
607 :    
608 : golsen 1.11
609 :     # Not sure why this was not done before
610 :    
611 :     sub add_pubmed_index {
612 :     my ( $rdbH, $html ) = @_;
613 :     return if ! $rdbH;
614 :     my $rtn = $rdbH->SQL( 'SHOW INDEX FROM dlits' );
615 :     push @$html, "<BR />Initial return value from 'SHOW INDEX FROM dlits' = $rtn\n";
616 :     if ( $rtn == 3 )
617 :     {
618 :     my $rtn = $rdbH->create_index( idx => "pubmed_in_dlits_ix",
619 :     tbl => "dlits",
620 :     type => "btree",
621 :     flds => "pubmed" );
622 :     $rtn = $rdbH->SQL( 'SHOW INDEX FROM dlits' );
623 :     push @$html, "<BR />Final return value from 'SHOW INDEX FROM dlits' = $rtn<BR />\n";
624 :     }
625 :     else
626 :     {
627 :     push @$html, "<BR />Index might already exist<BR />\n";
628 :     }
629 :     }

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