cgi-bin/insitu/detail/experiment.pl

   1
   2 use strict;
   3
   4 my $experiment_detail_page = CXGN::Insitu::Experiment_detail_page->new('insitu');
   5
   6 package CXGN::Insitu::Experiment_detail_page;
   7
   8 use CXGN::Insitu::Experiment;
   9 use CXGN::Insitu::Organism;
  10 use CXGN::Insitu::Toolbar;
  11 use SGN::Image;
  12 use CXGN::Tag;
  13 use CXGN::Page::FormattingHelpers qw / blue_section_html page_title_html /;
  14 use CXGN::People::Person;
  15
  16 use CatalystX::GlobalContext '$c';
  17
  18 use base qw / CXGN::Page::Form::SimpleFormPage /;
  19
  20 sub new {
  21     my $class = shift;
  22     my $self = $class->SUPER::new(@_);
  23     #$self->set_script_name("experiment.pl");
  24
  25     return $self;
  26 }
  27
  28 sub define_object {
  29     my $self = shift;
  30
  31     # call set_object_id, set_object and set_primary_key here
  32     # with the appropriate parameters.
  33     #
  34     my %args = $self->get_args();
  35     $self->set_object_id($args{experiment_id});
  36     $self->set_object(CXGN::Insitu::Experiment->new($self->get_dbh(),
  37                                                   $self->get_object_id())
  38                       );
  39     $self->set_primary_key("experiment_id");
  40     $self->set_owners($self->get_object()->get_user_id());
  41 }
  42
  43 sub delete {
  44     my $self = shift;
  45     $self->check_modify_privileges();
  46     my $experiment = $self->get_object();
  47     my $experiment_name = $experiment->get_name();
  48     my $error = $experiment->delete();
  49     $self->get_page()->message_page("The experiment $experiment_name has been deleted.");
  50 }
  51
  52
  53 sub generate_form {
  54     my $self = shift;
  55
  56     $self->init_form();
  57     my %args = $self->get_args();
  58     my $experiment = $self->get_object();
  59     my $experiment_id = $self->get_object_id();
  60
  61     # get some organism and probe information for the drop down menus
  62     #
  63     my ($organism_names_ref, $organism_ids_ref) = CXGN::Insitu::Organism::get_all_organisms($self->get_dbh());
  64     my ($probe_names_ref, $probe_ids_ref) = CXGN::Insitu::Probe::get_all_probes($self->get_dbh());
  65     my $types_names_ref = [ "Insitu", "Immunolocalization", "Histochemical localization" ];
  66
  67     my %field = (
  68                  experiment_name => "",
  69                  date => "",
  70                  tissue => "",
  71                  stage => "",
  72                  description => "",
  73                  probe_id => "",
  74                  probe_name => "",
  75                  organism_id => "",
  76                  user_id =>"",
  77                  );
  78     my $organism_name = "";
  79     my $organism_link = "";
  80     my $submitter;
  81     my $submitter_name="";
  82     my $probe_name="";
  83
  84     if ($self->get_action()=~/view|edit/i) {
  85         $field{type} = $experiment->get_type();
  86         $field{probe_id} = $experiment->get_probe_id();
  87         $field{user_id} = $experiment->get_user_id();
  88         $probe_name = $experiment->get_probe()->get_name();
  89         $field{organism_id} = $experiment -> get_organism_id();
  90         $organism_name = $experiment->get_organism();
  91         $organism_link = qq { <a href="organism.pl?organism_id=$field{organism_id}&amp;action=view">$organism_name</a> };
  92         $field{user_id} = $experiment->get_user_id();
  93         $submitter = CXGN::People::Person->new($self->get_dbh(), $field{user_id});
  94         $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
  95     }
  96 #     if ($self->get_action()=~/edit/i) {
  97 #       $submitter ||= CXGN::People::Person->new($field{user_id});
  98 #       $submitter_name ||= $submitter->get_first_name()." ".$submitter->get_last_name();
  99
 100 #     }
 101     if ($self->get_action()=~/store/i) {
 102         $probe_name = CXGN::Insitu::Probe->new($self->get_dbh(), $field{probe_id})->get_name();
 103         $organism_name = CXGN::Insitu::Organism->new($self->get_dbh(), $field{organism_id})->get_name();
 104         $submitter = CXGN::People::Person->new($self->get_dbh(), $field{user_id});
 105         $submitter_name = $submitter->get_first_name()." ".$submitter->get_last_name();
 106
 107     }
 108
 109     # generate the form using CXGN::Form.
 110     # setup the form using the CXGN::Page::Form functions for editable content
 111     #
 112     $self->get_form()-> add_field( display_name=>"Name", field_name=>"name", contents=>$field{name}, length=>20, object=>$experiment, getter=>"get_name", setter=>"set_name", validate=>"string" );
 113
 114     $self->get_form()-> add_field( display_name=>"Date", field_name=>"date", contents=>$field{date}, length=>15, object=>$experiment, getter=>"get_date", setter=>"set_date", validate=>"date");
 115
 116
 117
 118     $self->get_form -> add_field( display_name=>"Tissue", field_name=>"tissue", contents=> $field{tissue}, length=>15, object=>$experiment, getter=>"get_tissue", setter=>"set_tissue");
 119
 120     $self->get_form -> add_field( display_name=>"Stage", field_name=>"stage", contents=>$field{stage}, length=>20, object=>$experiment, getter=>"get_stage", setter=>"set_stage"  );
 121
 122     $self->get_form -> add_field( display_name=>"Other info", field_name=>"description", contents=> $field{description}, length=>30, object=>$experiment, getter=>"get_description", setter=>"set_description"  );
 123
 124     $self->get_form -> add_hidden( field_name => "experiment_id", contents=>$experiment_id );
 125
 126     $self->get_form -> add_hidden( field_name => "action", contents=>"store" );
 127
 128 #    if ($self->get_action() =~/edit|new|store/) {
 129
 130         $self->get_form -> add_select( display_name=>"Type", field_name=>"type", contents=>$field{type}, length=>20, object => $experiment, getter=>"get_type", setter=>"set_type", select_list_ref=>$types_names_ref, select_id_list_ref=>$types_names_ref );
 131
 132         $self->get_form->add_select( display_name=>"Organism", field_name=>"organism_id", contents=>$field{organism_id}, length=>10, object=>$experiment, getter=>"get_organism_id", setter=>"set_organism_id",  select_list_ref=>$organism_names_ref, select_id_list_ref=>$organism_ids_ref );
 133
 134         $self->get_form->add_select( display_name=>"Probe", field_name=>"probe_id", contents=>$field{probe_id}, length=>10, object=>$experiment, getter=>"get_probe_id", setter=>"set_probe_id", select_list_ref=>$probe_names_ref, select_id_list_ref=>$probe_ids_ref );
 135
 136  #   }
 137 #    elsif ($self->get_action() eq "view") {
 138
 139 #           $self->get_form -> add_field( display_name=>"Type", field_name=>"type", contents=>$field{type}, length=>20, object => $experiment, getter=>"get_type", setter=>"set_type" );
 140
 141 #       $self->get_form->add_field( display_name=>"Organism", field_name=>"organism_id", contents=>$organism_link, length=>20, validate=>"integer" );
 142
 143 #       $self->get_form()->add_field( display_name=>"Probe", field_name=>"probe_id", contents=> qq { <a href="probe.pl?probe_id=$field{probe_id}">$probe_name</a> } , length=>20, validate=>"integer" );
 144
 145 #     }
 146     $self->get_form()->add_label( display_name=>"Submitter",
 147                                   field_name=>"submitter",
 148                                   contents=>$submitter_name,
 149                                   );
 150
 151     if ($self->get_action()=~ /edit|view/) {
 152         $self->get_form()->from_database();
 153     }
 154     if ($self->get_action()=~/store/) {
 155         $self->get_form()->from_request(%args);
 156     }
 157
 158
 159 }
 160
 161 sub display_page {
 162     my $self = shift;
 163
 164     my %args = $self->get_args();
 165     my $experiment = $self->get_object();
 166     my $experiment_id = $self->get_object_id();
 167     my $user_id = $experiment->get_user_id();
 168     my $user = CXGN::People::Person->new($self->get_dbh(), $user_id);
 169
 170     # display and edit and delete link if we are not currently
 171     # in editing mode...
 172     #
 173     my $edit_link = "";
 174     my $delete_link = "";
 175     if ($self->get_action eq "new" ) {
 176         $edit_link = " <a href=\"/insitu/manage.pl\">[Cancel]</a>";
 177     }
 178     elsif ($self->get_action() eq "edit") {
 179         $edit_link = " <a href=\"experiment.pl?experiment_id=$experiment_id&amp;action=view\">[View]</a>";
 180     }
 181     else {
 182         $edit_link = " <a href=\"experiment.pl?experiment_id=$experiment_id&amp;action=edit\">[Edit]</a>";
 183         $delete_link = "<a href=\"experiment.pl?experiment_id=$experiment_id&amp;action=confirm_delete\">[Delete]</a>";
 184     }
 185
 186     # get some information that will be displayed statically only
 187     #
 188     my $page_title = page_title_html("<a href=\"/insitu/\">Insitu</a> Experiment \"".$experiment->get_name()."\"");
 189
 190     my $username = $experiment->get_user()->get_first_name()." ".$experiment->get_user()->get_last_name();
 191     if (!$username) {
 192         $username=$user->get_first_name()." ".$user->get_last_name();
 193     }
 194
 195     my $submit_user_id = $experiment->get_user()->get_sp_person_id();
 196     my $probe_id = $experiment->get_probe()->get_probe_id();
 197     my $probe_name = $experiment->get_probe()->get_name();
 198
 199     my $categories = ""; # $experiment->get_categories();
 200     my $organism_name = $experiment -> get_organism();
 201     my $organism_id = $experiment->get_organism_id();
 202     my $action = $self->get_action();
 203
 204     #print STDERR "*****   Organism: $organism_name id: $organism_id\n";
 205     my $image_count = $experiment->get_images();
 206
 207     $self->get_page()->add_style(text => ".centered {text-align: center}");
 208     $self->get_page()->header();
 209
 210     CXGN::Insitu::Toolbar::display_toolbar();
 211
 212     my $categories = "";
 213
 214     print <<HTML;
 215
 216     $page_title
 217     <h3>$action</h3>
 218
 219         <b>Experiment Info</b> $edit_link $delete_link<br /><br />
 220
 221 HTML
 222
 223     $self->get_form()->as_table();
 224
 225     my $tag_count = scalar($experiment->get_tags());
 226
 227     print qq { <br /><br /><b>Associated tags</b> [<a href="/tag/?experiment_id=$experiment_id&amp;action=new">add/remove</a>]: <b>$tag_count</b> };
 228
 229     foreach my $tag ($experiment->get_tags()) {
 230         print $tag->get_name()."  ";
 231     }
 232
 233         my $assoc_imgs_html = qq {<br /><br /><b>Associated images</b>: $image_count<br /><br />};
 234
 235         $assoc_imgs_html .= "<table width=\"90%\" cellpadding=\"0\" cellspacing=\"0\" class=\"centered\"><tr>\n";
 236
 237     my $i = 0;
 238     for ($i; $i< (my @image = $experiment->get_image_ids()); $i++) {
 239         my $image_id = $image[$i];
 240         my $image = SGN::Image->new( $self->get_dbh(), $image_id, $c );
 241         $assoc_imgs_html .= "<td valign=\"top\"><a href=\"/image/view/$image_id\">".$image->get_img_src_tag("small")."</a>&nbsp;<br />";
 242
 243         if ($self->get_action() eq "edit") {
 244             $assoc_imgs_html .= qq {<a href="/image/?image_id=$image_id&amp;type=experiment&amp;type_id=$experiment_id&amp;action=confirm_delete">Delete</a><br />};
 245         }
 246
 247         $assoc_imgs_html .= qq { </td><td width="20">&nbsp;</td> };
 248         if (($i+1) % 3 == 0 ) { $assoc_imgs_html .= "</tr><tr>"; }
 249
 250     }
 251     $assoc_imgs_html .= "<td></td></tr></table>"; #in xhtml 1.0+, a <tr> must have <td> children -- Evan, 1/6/07
 252
 253     print $assoc_imgs_html;
 254
 255     if ($self->get_action() eq "edit") {
 256         print qq {<a href="/image/add?type=experiment&amp;type_id=$experiment_id&amp;action=new">Add new image</a> };
 257     }
 258     $self->get_page()->footer();
 259 }