cgi-bin/image/add_image.pl

   1 use CatalystX::GlobalContext qw( $c );
   2
   3 =head1 NAME
   4
   5 add_image.pl - a web script to add image to the SGN database
   6
   7 =head1 DESCRIPTION
   8
   9 uploads an image to the SGN image database (the image table in the metadata schema) and places the image on the file system (using the conf object's image_dir parameters), resizes the image to thumbnail size etc. This is different from the deprecated CXGN::Insitu::Image, which had similar functionality, but was too insitu specific.
  10
  11 =head2 IMPORTANT NOTE
  12
  13 The uploaded images will be stored using the SGN::Image object. This object stores meta-information in the SGN database, and the image on disk. The file location is given by the $c SGN:Context  variable "image_dir". On the production server, this should be set to "/data/shared/website/image/image_files". To prevent different image to clobber the image_dir, that variable needs to be set to "/data/shared/website/image/image_files_sandbox" for the devel server. When the cxgn database is copied to sandbox, the corresponding image_dir needs to be copied over as well. Check these variables before adding images.
  14
  15 =head1 USAGE
  16
  17 This web script uses 3 stages for uploading an image, each step has its own set of parameters, explained below:
  18
  19 =head2 New image
  20
  21 This call will present the user with the option of selecting a file for upload.
  22
  23 =over 3
  24
  25 =item o
  26
  27 I<action>: needs to be set to "new"
  28
  29 =item o
  30
  31 I<type>: either experiment, individual, locus, or to be defined data types in the SGN database that can have associated images (fish etc).
  32
  33 =item o
  34
  35 I<type_id>: the primary key of the object of type "type" to which this image should be associated.
  36
  37 =item o
  38
  39 I<refering_page>: the page that requested the image upload.
  40
  41 =back
  42
  43 =head2 Confirm upload
  44
  45 before the image is uploaded, a confirm step occurs. The confirm step has to be called with the following parameters:
  46
  47 =over 3
  48
  49 =item o
  50
  51 I<action>: needs to be set to confirm
  52
  53 =item o
  54
  55 I<type>: see above
  56
  57 =item o
  58
  59 I<file>: the file to upload
  60
  61 =item o
  62
  63 I<refering_page>: The page that requested the image upload.
  64
  65 =back
  66
  67 =head2 Store image
  68
  69 This step will actually store the image in the SGN database. It then client_redirects to the image detail page for that image, such that hitting reload will not cause the image to be uploaded again.
  70
  71 =over 3
  72
  73 =item o
  74
  75 I<action>=store
  76
  77 =item o
  78
  79 I<type>: see above
  80
  81 =item o
  82
  83 I<type_id>: see above
  84
  85 =item o
  86
  87 I<refering_page>: the url of the refering page
  88
  89 =item o
  90
  91 I<temp_file>: the temp_file basename of the temporarily uploaded file in the designated temp_dir
  92
  93 =back
  94
  95 =head2 NOTES
  96
  97 Please note the following restrictions:
  98
  99 =over 4
 100
 101 =item o
 102
 103 Note that only post requests are supported for the image upload, with an enctype of multipart/form-data.
 104
 105 =item o
 106
 107 The user needs to be logged in and needs "submitter" privileges.
 108
 109 =back
 110
 111 =head1 SEE ALSO
 112
 113 The script that deals with displaying and editing the meta information is /image/index.pl .
 114 This script is based on the L<SGN::Image> object.
 115
 116 =head1 VERSION
 117
 118 Version 0.6, Dec 20, 2006.
 119
 120 =head1 AUTHOR(S)
 121
 122 Lukas Mueller (lam87@cornell.edu)
 123
 124 =head1 FUNCTIONS
 125
 126 The following functions are documented in this script:
 127
 128 =cut
 129
 130 use strict;
 131
 132 use CXGN::DB::Connection;
 133 use CXGN::Page;
 134 use CXGN::Page::FormattingHelpers qw / blue_section_html page_title_html / ;
 135 use SGN::Image;
 136 use CXGN::People::Person;
 137 use CXGN::Contact;
 138
 139 # get the parameters.
 140 # legal parameters are:
 141 #  action: new upload
 142 #  image_id: a valid image_id
 143 #  experiment_id: a valid experiment_id
 144 #  upload_file: the file to be uploaded, if action=upload.
 145 #
 146
 147 my $request = shift;
 148
 149
 150 my $page = CXGN::Page->new();
 151
 152 my %args = $page->get_all_encoded_arguments;
 153
 154 # get db connection
 155 #
 156 my $dbh = CXGN::DB::Connection->new();
 157
 158 # get the sp_person_id if user is logged in for actions add and upload.
 159 #
 160 my $user = undef;
 161 my $sp_person_id=undef;
 162 if ($args{action} =~/new|confirm|store/i ) {
 163     my $login = CXGN::Login->new($dbh);
 164     $sp_person_id = $login ->verify_session();
 165     $user =  CXGN::People::Person->new($dbh, $sp_person_id);
 166     #$sp_person_id= $user->get_sp_person_id();
 167     if ($user->get_user_type() !~ /curator|submitter/) {
 168         $page->message_page("You do not have sufficient privileges to upload images. You need an account of type 'submitter'. Please contact SGN to change your account type. Sorry.");
 169     }
 170 }
 171 else {
 172     $page->message_page("Unknown action $args{action}. What do you want to do exactly?");
 173 }
 174
 175 # create an new image object and go through the different
 176 # possible actions. Emit error pages if needed.
 177 #
 178 my $image = SGN::Image->new($dbh);
 179
 180 if ($args{action} eq "new") {
 181     # check stuff
 182
 183     # do stuff
 184     add_dialog($page, $image, %args);
 185
 186 }
 187 elsif ($args{action} eq "confirm") {
 188     # check stuff
 189
 190     # do stuff
 191     confirm($dbh, $page, %args);
 192 }
 193 elsif ($args{action} eq "store") {
 194     # check stuff
 195
 196     # do stuff
 197     $args{sp_person_id} = $sp_person_id ;
 198     store($dbh, $page, $image, %args);
 199 }
 200 else {
 201     $page->message_page("No valid parameters were supplied.");
 202 }
 203
 204
 205 =head2 add_dialog
 206
 207  Usage:        add_dialog($page, $image, %args)
 208  Desc:         Add dialog displays a page allowing to select and submit
 209                an image file
 210  Ret:
 211  Args:         $page: a page object
 212                $image: an image object (empty)
 213                $args{type}: either "individual" or "experiment"
 214                $args{type_id}: the primary key identifying the object
 215                of type $args{type}
 216                $args{refering_page}: The page that has called the
 217                add_image script.
 218                This is used to show a link to the calling script.
 219  Side Effects:
 220  Example:
 221
 222 =cut
 223
 224 sub add_dialog {
 225     my $page = shift;
 226     my $image = shift;
 227     my %args = @_;
 228
 229     $page->header();
 230
 231     print page_title_html("Add image to $args{type} $args{type_id}" );
 232
 233     print qq {
 234
 235         <p class="boxbgcolor2">Note: By pressing the "Upload" button, you are considered to be the copyright owner of the image being uploaded and that you grant a non-exclusive license to SGN to display and use the image on SGN webpages and materials related to SGN.<br /></p>
 236         <p> Supported file formats include .jpg. .jpeg, .gif, .png, .pdf, .ps,
 237         .eps <br></p>
 238         <form action="add_image.pl" method="post" enctype="multipart/form-data" >
 239             Upload an image, and associated with object <b>$args{type}</b> id $args{type_id}<br /><br />
 240             <input type="file" name="file" value="Choose image file" />
 241             <input type="hidden" name="action" value="confirm" /><br /><br />
 242             <input type="hidden" name="type" value="$args{type}" />
 243             <input type="hidden" name="type_id" value="$args{type_id}" />
 244             <input type="hidden" name="refering_page" value="$args{refering_page}" />
 245             <input type="submit" value="Upload" />
 246          </form>
 247      };
 248
 249     if ($args{refering_page}) { print "<a href=\"$args{refering_page}\">Go back</a>"; }
 250
 251     $page->footer();
 252 }
 253
 254 =head2 confirm
 255
 256  Usage:
 257  Desc:
 258  Ret:
 259  Args:
 260  Side Effects:
 261  Example:
 262
 263 =cut
 264
 265 sub confirm {
 266     my $dbh = shift;
 267     my $page = shift;
 268     my %args = @_;
 269
 270
 271     # deal with the upload options
 272     #
 273     my $upload = $page->get_upload();
 274     my $upload_fh;
 275
 276     if (defined $upload) {
 277
 278
 279         $args{temp_file} = $image->apache_upload_image($upload);
 280         #if ($temp_file eq "-1") {
 281         #    $page->message_page("It seems that this file is in the process of being uploaded. Please do not upload files several times!!!! ");
 282         #}
 283
 284         my $temp_file_base = File::Basename::basename($args{temp_file});
 285         my $sample_image = $temp_file_base;
 286
 287         $page->header();
 288
 289         my $filename_validation_msg =  validate_image_filename($temp_file_base);
 290         if ( $filename_validation_msg )  { #if non-blank, there is a problem with Filename, print messages
 291             #print STDERR "Invalid Upload Filename Attempt: $temp_file_base, $filename_validation_msg \n";
 292             print qq { There is a problem with the image file you selected: $temp_file_base <br />};
 293             print qq { Error:  };
 294             print $filename_validation_msg;
 295             print qq {<br />};
 296             unlink $args{temp_file};  # remove upload! prevents more errors on item we have rejected
 297             if ($args{refering_page}) { print "<a href=\"$args{refering_page}\">[Return]</a><br /><br />\n"; }
 298         } else {
 299         ### deanx Testing --  this is trashable
 300         if   ($temp_file_base =~ /(.*)\.(.{1,4})$/ ) {
 301            if ( $2 =~ /[pdf|ps|eps]/i ) {
 302              SGN::Image::iconify_file($args{temp_file});
 303              $sample_image = $temp_file_base.'.jpg';
 304              }
 305          }
 306
 307         print qq { The image uploaded is shown below. Please click on "Store in SGN database" to permanently store the image in the database. <br /> };
 308
 309         print "<br /><br />\n";
 310         if ($args{type} && $args{type_id}) { print "<b>Association</b> $args{type} id $args{type_id}<br /><br />\n"; }
 311
 312         print "Submitter: $sp_person_id<br />\n";
 313
 314         print qq {
 315             <form method="get">
 316                 <input type="hidden" name="temp_file" value="$temp_file_base" />
 317                 <input type="hidden" name="action" value="store" />
 318                 <input type="hidden" name="type" value="$args{type}" />
 319                 <input type="hidden" name="type_id" value="$args{type_id}" />
 320                 <input type="submit" value="Store in SGN database" />
 321
 322                 </form>
 323             };
 324
 325         if ($args{refering_page}) { print "<a href=\"$args{refering_page}\">[Cancel]</a><br /><br />\n"; }
 326
 327         print qq { <img src="/documents/tempfiles/temp_images/$sample_image" /> };
 328
 329         $page->footer();
 330
 331        } # Ok filename
 332     }
 333     else {
 334         $page->error_page("A freakin error occurred!");
 335     }
 336
 337 }
 338
 339
 340 =head2 store
 341
 342  Usage:
 343  Desc:
 344  Ret:
 345  Args:         $dbh - a database handle
 346                $page - a page object
 347                $image - an image object
 348                %args, with the following key/values:
 349                       $args{file} -
 350                       $args{temp_file} -
 351                       $args{type} -
 352                       $args{type_id} -
 353                       $args{refering_page} -
 354                       $args{sp_person_id} -
 355  Side Effects:
 356  Example:
 357
 358 =cut
 359
 360 #  store($dbh, $page, $file, $image, $type, $type_id, $refering_page, $sp_person_id);
 361 sub store {
 362     my ($dbh, $page, $image, %args) = @_;
 363     my $sp_person_id = $args{sp_person_id};
 364
 365     my $temp_image_dir = $c->get_conf("basepath")."/".$c->get_conf("tempfiles_subdir") ."/temp_images";
 366
 367     $image -> set_sp_person_id($sp_person_id);
 368
 369     if ((my $err = $image->process_image($temp_image_dir."/".$args{temp_file}, $args{type}, $args{type_id}))<=0) {
 370         $page->message_page("An error occurred during the upload. Is the file you are uploading an image file? [$err] ");
 371         exit();
 372     }
 373
 374     # set some image attributes...
 375     # the image owner...
 376     #print STDERR "Setting the submitter information in the image object...\n";
 377
 378     $image -> set_name($args{file});
 379
 380
 381     $image->store();
 382
 383     send_image_email($dbh, $image, $sp_person_id, %args);
 384     #remove the temp_file
 385     #
 386     unlink ($temp_image_dir."/".$args{temp_file});
 387
 388     $args{image_id}=$image->get_image_id();
 389
 390
 391     # go to the image detail page
 392     # open for editing.....
 393     $page->client_redirect("/image/?image_id=$args{image_id}&action=edit");
 394 }
 395
 396 =head2 store
 397
 398  Usage:  validate_image_filename($filename);
 399  Desc:   Validate the Upload Image file string seems reasonable
 400  Ret:    Returns 0 if file name OK, otherwise returns appropriate error msg
 401  Args:   $filename
 402
 403  Side Effects:
 404  Example:
 405
 406 =cut
 407
 408 sub validate_image_filename {
 409   my $fn = shift;
 410   my %file_types = ( '.jpg' => 'JPEG file',
 411                      '.jpeg' => 'JPEG file',
 412                      '.gif' => 'GIF file',
 413                      '.pdf' => 'PDF file',
 414                      '.ps'  => 'PS file',
 415                      '.eps' => 'EPS file',
 416                      '.png' => 'PNG file');
 417
 418
 419
 420   # first test is non-acceptable characters in filename
 421   my $OK_CHARS='-a-zA-Z0-9_.@\ '; # as recommend by CERT, test for what you will allow
 422   my $test_fn = $fn;
 423   $test_fn =~ s/[^$OK_CHARS]/_/go;
 424   if ( $fn ne $test_fn ) {
 425       #print STDERR "Upload Attempt with bad shell characters: $fn \n";
 426        return "Invalid characters found in filename, must not contain
 427         characters <b>\& ; : \` \' \\ \| \* \? ~ ^ < > ( ) [ ] { } \$</b>" ;
 428      }
 429
 430
 431
 432   my $ext;
 433   if ($fn =~ m/^(.*)(\.\S{1,4})\r*$/) {
 434       $ext = lc ($2);
 435       #print STDERR "Upload Attempt with disallowed filename extension: $fn Extension: $ext\n";
 436       return "File Type must be one of: .png, .jpg, .jpeg, .gif, .pdf, .ps, or .eps" unless exists $file_types{$ext};
 437     } else {
 438       #print STDERR "Upload Attempt with filename extension we could not parse: $fn \n";
 439       return "File Type must be one of: .png, .jpg, .jpeg, .gif, .pdf, .ps, or .eps";
 440     }
 441
 442   return 0;  # FALSE, if passes all tests
 443 }
 444
 445 sub send_image_email {
 446     my $dbh = shift;
 447     my $image = shift;
 448     my $sp_person_id = shift;
 449     my %args = @_;
 450     my $refering_page=$args{refering_page};
 451     my $type= $args{type};  #locus or...?
 452     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 453     my $image_id = $image->get_image_id();
 454     my $action = $args{action};
 455     #my $sp_person_id = $args{sp_person_id};
 456
 457     my $person= CXGN::People::Person->new($dbh, $sp_person_id);
 458     my $user=$person->get_first_name()." ".$person->get_last_name();
 459
 460     my $type_link;
 461
 462
 463     my $user_link = qq | http://sgn.cornell.edu/solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
 464     my $usermail=$person->get_contact_email();
 465     my $image_link = qq |http://sgn.cornell.edu/image/?image_id=$image_id|;
 466     if ($type eq 'locus') {
 467         $type_link = qq | http://sgn.cornell.edu/phenome/locus_display.pl?locus_id=$type_id|;
 468     }
 469 #    elsif ($type eq 'allele') {
 470 #       $type_link = qq | http://sgn.cornell.edu/phenome/allele.pl?allele_id=$type_id|;
 471 #     }
 472 #     elsif ($type eq 'population') {
 473 #       $type_link = qq | http://sgn.cornell.edu/phenome/population.pl?population_id=$type_id|;
 474 #     }
 475
 476     my $fdbk_body;
 477     my $subject;
 478
 479     if ($action eq 'store') {
 480
 481         $subject="[New image associated with $type: $type_id]";
 482         $fdbk_body="$user ($user_link) has associated image $image_link \n with $type: $type_link";
 483    }
 484     elsif($action eq 'delete') {
 485
 486
 487         $subject="[A image-$type association removed from $type: $type_id]";
 488         $fdbk_body="$user ($user_link) has removed publication $image_link \n from $type: $type_link";
 489     }
 490
 491     CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 492
 493 }