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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | =head1 Generate NMPDR Web Page Includes | ||
| 4 : | |||
| 5 : | This script generates the include files for the NMPDR cover pages. The include | ||
| 6 : | files go in the C<html/includes> directory for the current NMPDR, and are | ||
| 7 : | based on data in the Sprout database. They need to be generated after the | ||
| 8 : | Sprout database is loaded, but before the cover pages are put online. | ||
| 9 : | |||
| 10 : | The include files generated are: | ||
| 11 : | |||
| 12 : | =over 4 | ||
| 13 : | |||
| 14 : | =item version.inc | ||
| 15 : | |||
| 16 : | Displays the version date, the genome counts, the number of subsystems, | ||
| 17 : | and the number of new annotations. This file is included in the | ||
| 18 : | C<index.php> document. | ||
| 19 : | |||
| 20 : | parrello | 1.11 | =item forms/all_genomes.inc |
| 21 : | parrello | 1.1 | |
| 22 : | Displays a form allowing the user to select an organism and see a summary of | ||
| 23 : | its subsystems and reactions. This file is included in the | ||
| 24 : | C<content/subsystems.php> document. | ||
| 25 : | |||
| 26 : | =item sproutdb.inc | ||
| 27 : | |||
| 28 : | Displays the documentation for the Sprout database. This file is included in | ||
| 29 : | the C<content/docs.php> document. | ||
| 30 : | |||
| 31 : | =back | ||
| 32 : | |||
| 33 : | The currently-supported command-line options are as follows. | ||
| 34 : | |||
| 35 : | =over 4 | ||
| 36 : | |||
| 37 : | =item user | ||
| 38 : | |||
| 39 : | Name suffix to be used for log files. If omitted, the PID is used. | ||
| 40 : | |||
| 41 : | =item trace | ||
| 42 : | |||
| 43 : | Numeric trace level. A higher trace level causes more messages to appear. The | ||
| 44 : | default trace level is 2. Tracing will be directly to the standard output | ||
| 45 : | as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory, | ||
| 46 : | where I<User> is the value of the B<user> option above. | ||
| 47 : | |||
| 48 : | =item sql | ||
| 49 : | |||
| 50 : | If specified, turns on tracing of SQL activity. | ||
| 51 : | |||
| 52 : | =item background | ||
| 53 : | |||
| 54 : | Save the standard and error output to files. The files will be created | ||
| 55 : | in the FIG temporary directory and will be named C<err>I<User>C<.log> and | ||
| 56 : | C<out>I<User>C<.log>, respectively, where I<User> is the value of the | ||
| 57 : | B<user> option above. | ||
| 58 : | |||
| 59 : | =item h | ||
| 60 : | |||
| 61 : | Display this command's parameters and options. | ||
| 62 : | |||
| 63 : | =item target | ||
| 64 : | |||
| 65 : | parrello | 1.2 | Target directory for the include files. The default is C<includes> in the |
| 66 : | C<$FIG_Config::nmpdr_pages> directory. | ||
| 67 : | parrello | 1.1 | |
| 68 : | =back | ||
| 69 : | |||
| 70 : | =cut | ||
| 71 : | |||
| 72 : | use strict; | ||
| 73 : | use Tracer; | ||
| 74 : | use DocUtils; | ||
| 75 : | use TestUtils; | ||
| 76 : | use Cwd; | ||
| 77 : | use File::Copy; | ||
| 78 : | use File::Path; | ||
| 79 : | use FIG; | ||
| 80 : | parrello | 1.3 | use CGI qw(:standard); |
| 81 : | parrello | 1.1 | |
| 82 : | # Get the command-line options and parameters. | ||
| 83 : | my ($options, @parameters) = StandardSetup([qw(Sprout ERDB SFXlate) ], | ||
| 84 : | { | ||
| 85 : | parrello | 1.10 | trace => [2, 'tracing level'], |
| 86 : | parrello | 1.2 | target => ["$FIG_Config::nmpdr_pages/includes", |
| 87 : | parrello | 1.1 | 'output directory'], |
| 88 : | }, | ||
| 89 : | "<version date>", | ||
| 90 : | @ARGV); | ||
| 91 : | |||
| 92 : | use SFXlate; | ||
| 93 : | |||
| 94 : | # Get the target directory. | ||
| 95 : | my $targetDir = $options->{target}; | ||
| 96 : | parrello | 1.4 | # Verify the parameters. |
| 97 : | if (! $parameters[0]) { | ||
| 98 : | Confess("Please specify a version date."); | ||
| 99 : | } elsif (! -d $targetDir) { | ||
| 100 : | Confess("Target directory $targetDir does not exist."); | ||
| 101 : | } else { | ||
| 102 : | parrello | 1.5 | Trace("Output going to $targetDir.") if T(2); |
| 103 : | parrello | 1.4 | # Get the Sprout object. |
| 104 : | my $sfx = SFXlate->new_sprout_only(); | ||
| 105 : | parrello | 1.7 | # Get the old Sprout. |
| 106 : | parrello | 1.12 | my $oldSprout = SFXlate->old_sprout_only(); |
| 107 : | parrello | 1.4 | # Create the counts file. |
| 108 : | parrello | 1.7 | CreateCounts($sfx, $oldSprout, $parameters[0], "$targetDir/version.inc"); |
| 109 : | parrello | 1.4 | # Create the subsystem summary file. |
| 110 : | parrello | 1.12 | CreateSubForm($sfx, "$targetDir/forms/subsystems.inc"); |
| 111 : | # Create the organism summary file. | ||
| 112 : | CreateOrgForm($sfx, "$targetDir/forms/all_genomes.inc"); | ||
| 113 : | parrello | 1.4 | # Create the database documentation file. |
| 114 : | CreateSproutDoc($sfx, "$targetDir/sproutdb.inc"); | ||
| 115 : | # Tell the user we're done. | ||
| 116 : | Trace("File creation complete.") if T(2); | ||
| 117 : | } | ||
| 118 : | parrello | 1.1 | |
| 119 : | =head3 CreateCounts | ||
| 120 : | |||
| 121 : | C<< CreateCounts($fig, $fileName); >> | ||
| 122 : | |||
| 123 : | Create the count and version display for the front page of the NMPDR. | ||
| 124 : | |||
| 125 : | =over 4 | ||
| 126 : | |||
| 127 : | =item sfx | ||
| 128 : | |||
| 129 : | A Sprout object for accessing the database. | ||
| 130 : | |||
| 131 : | parrello | 1.7 | =item oldSfx |
| 132 : | parrello | 1.1 | |
| 133 : | parrello | 1.7 | A Sprout object for accessing the previous database. |
| 134 : | parrello | 1.1 | |
| 135 : | =item versionDate | ||
| 136 : | |||
| 137 : | The string to be used for the version date. | ||
| 138 : | |||
| 139 : | =item fileName | ||
| 140 : | |||
| 141 : | The name of the output file. | ||
| 142 : | |||
| 143 : | =back | ||
| 144 : | |||
| 145 : | =cut | ||
| 146 : | |||
| 147 : | sub CreateCounts { | ||
| 148 : | # Get the parameters. | ||
| 149 : | parrello | 1.7 | my ($sfx, $oldSfx, $versionDate, $fileName) = @_; |
| 150 : | parrello | 1.1 | # Open the output file. |
| 151 : | my $handle = Open(undef, ">$fileName"); | ||
| 152 : | # Start the heading. | ||
| 153 : | print $handle "<h3 class=\"home\">Version $versionDate\n"; | ||
| 154 : | # Get the counts. | ||
| 155 : | my @counts = $sfx->GenomeCounts(); | ||
| 156 : | my @names = qw(archaeal bacterial eukaryal viral environmental); | ||
| 157 : | # Get a list of named counts for all the categories with nonzero values. | ||
| 158 : | my @namedCounts = (); | ||
| 159 : | for (my $i = 0; $i <= $#names; $i++) { | ||
| 160 : | if ($counts[$i]) { | ||
| 161 : | push @namedCounts, "$counts[$i] $names[$i]"; | ||
| 162 : | } | ||
| 163 : | } | ||
| 164 : | # Form the named counts into English, which is a very complicated process. | ||
| 165 : | my $output = "Includes $namedCounts[0]"; | ||
| 166 : | for (my $i = 1; $i < $#namedCounts; $i++) { | ||
| 167 : | $output .= ", $namedCounts[$i]"; | ||
| 168 : | } | ||
| 169 : | if ($#namedCounts > 0) { | ||
| 170 : | $output .= ", and $namedCounts[$#namedCounts]"; | ||
| 171 : | } | ||
| 172 : | $output .= " genomes."; | ||
| 173 : | # Output the counts. | ||
| 174 : | print $handle "<br />$output"; | ||
| 175 : | # Get the number of subsystems. | ||
| 176 : | my $subsystems = $sfx->GetCount(['Subsystem'], "", []); | ||
| 177 : | parrello | 1.9 | print $handle "<br />$subsystems active subsystems"; |
| 178 : | parrello | 1.13 | # Count the number of new annotations, genomes, and features. |
| 179 : | parrello | 1.8 | my %things = ( Annotation => 'annotations', |
| 180 : | Feature => 'features', | ||
| 181 : | Genome => 'organisms' | ||
| 182 : | ); | ||
| 183 : | for my $thing (sort keys %things) { | ||
| 184 : | my $newCount = $sfx->GetCount([$thing], "", []); | ||
| 185 : | my $oldCount = $oldSfx->GetCount([$thing], "", []); | ||
| 186 : | my $delta = $newCount - $oldCount; | ||
| 187 : | # Only display them if there's a reasonable number. | ||
| 188 : | if ($delta > 5) { | ||
| 189 : | parrello | 1.9 | print $handle ", $delta new $things{$thing}"; |
| 190 : | parrello | 1.8 | } |
| 191 : | parrello | 1.1 | } |
| 192 : | parrello | 1.13 | # Add the docking results. |
| 193 : | my $pdbCount = $sfx->GetCount(['PDB'], "PDB(docking-count) > ?", [0]); | ||
| 194 : | print $handle ", $pdbCount PDBs with in silico docking results"; | ||
| 195 : | parrello | 1.1 | # Terminate the heading. |
| 196 : | print $handle ".</h3>\n"; | ||
| 197 : | # Close the output file. | ||
| 198 : | close $handle; | ||
| 199 : | } | ||
| 200 : | |||
| 201 : | =head3 CreateSubForm | ||
| 202 : | |||
| 203 : | C<< CreateSubForm($sfx, $fileName); >> | ||
| 204 : | |||
| 205 : | Output the subsystem summary form. The subsystem summary form allows the user | ||
| 206 : | to select an organism and view a summary of its subsystems. | ||
| 207 : | |||
| 208 : | =over 4 | ||
| 209 : | |||
| 210 : | =item sfx | ||
| 211 : | |||
| 212 : | A Sprout object that can be used to access the NMPDR database. | ||
| 213 : | |||
| 214 : | =item fileName | ||
| 215 : | |||
| 216 : | The name of the file to create with the form HTML in it. | ||
| 217 : | |||
| 218 : | =back | ||
| 219 : | |||
| 220 : | =cut | ||
| 221 : | |||
| 222 : | sub CreateSubForm { | ||
| 223 : | # Get the parameters. | ||
| 224 : | my ($sfx, $fileName) = @_; | ||
| 225 : | parrello | 1.3 | # Start the form. |
| 226 : | my @page = (); | ||
| 227 : | push @page, start_form({method => "post", action => "../FIG/genome_statistics.cgi", | ||
| 228 : | enctype=> "application/x-www-form-urlencoded"}); | ||
| 229 : | # Make sure the script knows it's for SPROUT. | ||
| 230 : | push @page, input({type => "hidden", name => "SPROUT", value => "1"}); | ||
| 231 : | # Surround the form parts with a table. | ||
| 232 : | push @page, "<table><tr><td>"; | ||
| 233 : | parrello | 1.12 | # Add the buttons. |
| 234 : | push @page, CGI::p("For the genome selected below, show " . | ||
| 235 : | input({type => "submit", name => "show_subsystems", | ||
| 236 : | value => "Subsystems", class => "button"}) . | ||
| 237 : | input({type => "submit", name => "show_reactions", | ||
| 238 : | value => "Reactions", class => "button"})); | ||
| 239 : | # End the first table cell. | ||
| 240 : | push @page, "</td></tr><tr><td>"; | ||
| 241 : | parrello | 1.3 | # Create the gene menu. |
| 242 : | push @page, $sfx->GeneMenu({ name => 'genome', size => 10 }, "", []); | ||
| 243 : | parrello | 1.12 | # Close the table. |
| 244 : | push @page, "</td></tr></table>"; | ||
| 245 : | # Close the form. | ||
| 246 : | push @page, end_form(); | ||
| 247 : | # Put together all the pieces. | ||
| 248 : | my $wholePage = join("\n", @page); | ||
| 249 : | # Open the output file. | ||
| 250 : | my $handle = Open(undef, ">$fileName"); | ||
| 251 : | # Write out the HTML. | ||
| 252 : | print $handle $wholePage; | ||
| 253 : | # Close the file. | ||
| 254 : | close $handle; | ||
| 255 : | |||
| 256 : | } | ||
| 257 : | |||
| 258 : | =head3 CreateOrgForm | ||
| 259 : | |||
| 260 : | C<< CreateOrgForm($sfx, $fileName); >> | ||
| 261 : | |||
| 262 : | Output the organism summary form. The organism summary form allows the user | ||
| 263 : | to select an organism and view its statistics. | ||
| 264 : | |||
| 265 : | =over 4 | ||
| 266 : | |||
| 267 : | =item sfx | ||
| 268 : | |||
| 269 : | A Sprout object that can be used to access the NMPDR database. | ||
| 270 : | |||
| 271 : | =item fileName | ||
| 272 : | |||
| 273 : | The name of the file to create with the form HTML in it. | ||
| 274 : | |||
| 275 : | =back | ||
| 276 : | |||
| 277 : | =cut | ||
| 278 : | |||
| 279 : | sub CreateOrgForm { | ||
| 280 : | # Get the parameters. | ||
| 281 : | my ($sfx, $fileName) = @_; | ||
| 282 : | # Start the form. | ||
| 283 : | my @page = (); | ||
| 284 : | push @page, start_form({method => "post", action => "../FIG/genome_statistics.cgi", | ||
| 285 : | enctype=> "application/x-www-form-urlencoded"}); | ||
| 286 : | # Make sure the script knows it's for SPROUT. | ||
| 287 : | push @page, input({type => "hidden", name => "SPROUT", value => "1"}); | ||
| 288 : | # Surround the form parts with a table. | ||
| 289 : | push @page, "<table><tr><td>"; | ||
| 290 : | # Add the button. | ||
| 291 : | push @page, CGI::p("Search or view statistics for the genome selected below " . | ||
| 292 : | input({type => "submit", name => "statistics", | ||
| 293 : | value => "Go", class => "button"})); | ||
| 294 : | parrello | 1.3 | # End the first table cell. |
| 295 : | push @page, "</td></tr><tr><td>"; | ||
| 296 : | parrello | 1.12 | # Create the gene menu. |
| 297 : | push @page, $sfx->GeneMenu({ name => 'genome', size => 10 }, "", []); | ||
| 298 : | parrello | 1.3 | # Close the table. |
| 299 : | push @page, "</td></tr></table>"; | ||
| 300 : | # Close the form. | ||
| 301 : | push @page, end_form(); | ||
| 302 : | # Put together all the pieces. | ||
| 303 : | my $wholePage = join("\n", @page); | ||
| 304 : | parrello | 1.1 | # Open the output file. |
| 305 : | my $handle = Open(undef, ">$fileName"); | ||
| 306 : | parrello | 1.3 | # Write out the HTML. |
| 307 : | print $handle $wholePage; | ||
| 308 : | parrello | 1.1 | # Close the file. |
| 309 : | close $handle; | ||
| 310 : | |||
| 311 : | } | ||
| 312 : | |||
| 313 : | =head3 CreateSproutDoc | ||
| 314 : | |||
| 315 : | C<< CreateSproutDoc($sfx, $fileName); >> | ||
| 316 : | |||
| 317 : | Output the Sprout database documentation. | ||
| 318 : | |||
| 319 : | =over 4 | ||
| 320 : | |||
| 321 : | =item sfx | ||
| 322 : | |||
| 323 : | A Sprout object that can be used to access the NMPDR database. | ||
| 324 : | |||
| 325 : | =item fileName | ||
| 326 : | |||
| 327 : | The name of the file to create with the documentation in it. | ||
| 328 : | |||
| 329 : | =back | ||
| 330 : | |||
| 331 : | =cut | ||
| 332 : | |||
| 333 : | sub CreateSproutDoc { | ||
| 334 : | # Get the parameters. | ||
| 335 : | my ($sfx, $fileName) = @_; | ||
| 336 : | # Open the output file. | ||
| 337 : | my $handle = Open(undef, ">$fileName"); | ||
| 338 : | # Write the Sprout database document into it. | ||
| 339 : | print $handle $sfx->DisplayMetaData(); | ||
| 340 : | # Close the file. | ||
| 341 : | close $handle; | ||
| 342 : | } | ||
| 343 : | |||
| 344 : | |||
| 345 : | |||
| 346 : | 1; |
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