cgi-bin/chado/fetch_pubmed.pl

   1
   2 use strict;
   3
   4
   5 use CXGN::Page;
   6 use CXGN::Page::FormattingHelpers qw / info_section_html page_title_html html_optional_show/;
   7 use CXGN::Chado::Publication;
   8
   9 use CXGN::Login;
  10 use CXGN::People;
  11 use CXGN::Contact;
  12 use CXGN::Tools::Pubmed;
  13 use CXGN::Tools::Text qw / sanitize_string /;
  14 use CXGN::DB::Connection;
  15
  16 use base qw / CXGN::DB::ModifiableI /;
  17
  18 my $page=CXGN::Page->new("Fetch PubMed","Naama");
  19 my $dbh = CXGN::DB::Connection->new();
  20
  21 my $logged_in_person_id=CXGN::Login->new($dbh)->verify_session();
  22 my $logged_in_user=CXGN::People::Person->new($dbh, $logged_in_person_id);
  23 my $logged_in_person_id=$logged_in_user->get_sp_person_id();
  24 my $logged_in_username=$logged_in_user->get_first_name()." ".$logged_in_user->get_last_name();
  25 my $logged_in_user_type=$logged_in_user->get_user_type();
  26
  27 #only curators can access this page
  28 if($logged_in_user_type eq 'curator') {
  29     $page->header();
  30     my %args=$page->get_all_encoded_arguments();
  31     my $ids = $args{"pubmed_ids"};
  32     my $curator_id= $args{curator_id};
  33     my $action = $args{action};
  34
  35     my @fail=();
  36     if($ids) {
  37         my @pubmeds = split (/\r\n/, $ids);
  38         if(@fail) {
  39             my $fail_str="";
  40             foreach(@fail) {    $fail_str .= "<li>$_</li>\n"; }
  41             print <<END_HTML;
  42
  43             <table width=80% align=center>
  44             <tr><td>
  45             <p>Could not feth pubmed ids  for the following reasons</p>
  46             <ul>
  47             $fail_str
  48             </ul>
  49             <p>Please use your browser\'s back button to try again.</p>
  50             </td></tr>
  51             <tr><td><br /></td></tr>
  52             </table>
  53 END_HTML
  54         }
  55         else {
  56             print qq | <br/><b> Fetched the following  publications from PubMed</b> | ;
  57             my $pubmed_string;
  58             my $count=0;
  59             foreach my $pubmed (@pubmeds) {
  60                 my $pub = CXGN::Chado::Publication->new($dbh);
  61                 $pub->set_accession($pubmed);
  62                 CXGN::Tools::Pubmed->new($pub); #call eutils and populates the publication object with all necessary fields
  63                 if ($pub->get_title()) {
  64                     $count++;
  65                     my $pub_ref=$pub->print_pub_ref();
  66                     $pubmed_string .= $pubmed . "|";
  67                     print <<END_HTML;
  68                     <table width=80% align=center>
  69                         <tr><td><p><b>$count.</b> $pub_ref (PMID:$pubmed)</p></td></tr>
  70                         <tr><td><br /></td></tr>
  71                         </table>
  72 END_HTML
  73                 }
  74             }
  75             print <<END_HTML;
  76             <form method="post" action="">
  77                 <input type="submit" name="action" value="Confirm store">
  78                 <input type = "hidden" name="curator_id" value=$curator_id>
  79                 <input type = "hidden" name="publications" value=$pubmed_string>
  80                 </form><br>
  81                 <a href="javascript:history.back(1)">Go back without storing the publications</a>
  82 END_HTML
  83
  84         }
  85
  86     }elsif ($action eq 'Confirm store') {
  87
  88         my $ids = $args{publications};
  89         my $curator_id = $args{curator_id} ;
  90
  91         my @pubmeds  = split (/\|/, $ids);
  92         my $count=0;
  93         print qq | <br/><b> stored the following  publications from PubMed</b><br /> | ;
  94         print qq| (assigned to curator $curator_id) | ;
  95         #chop $ids;
  96         foreach my $pubmed (@pubmeds) {
  97                 #$pubmed =~ s/ +//g;
  98                 my $pub = CXGN::Chado::Publication->new($dbh);
  99                 $count++;
 100                 $pub->set_accession($pubmed);
 101                 $pub->add_dbxref("PMID:$pubmed");
 102                 CXGN::Tools::Pubmed->new($pub); #call eutils and populates the publication object with all necessary fields
 103                 my $pub_ref=$pub->print_pub_ref();
 104                 my $e_id = $pub->get_eid;
 105                 if ($e_id) {
 106                     $pub->add_dbxref("DOI:$e_id");
 107                 }
 108                 $pub->store();
 109
 110                 unless ($pub->is_curated() ) {
 111                     $pub->set_sp_person_id($logged_in_person_id);
 112                     $pub->set_curator_id($curator_id); #
 113                     $pub->set_status('pending');
 114                     $pub->store_pub_curator();
 115                     $pub->d("Assigned publication $pubmed to curator $curator_id");
 116                 }
 117                 print <<END_HTML;
 118                 <table width=80% align=center>
 119                     <tr><td><p><b>$count.</b> $pub_ref (PMID:$pubmed)</p></td></tr>
 120                     <tr><td><br /></td></tr>
 121                     </table>
 122 END_HTML
 123             }
 124         print qq | <a href="/chado/fetch_pubmed.pl">Go back to fetch  publications page </a ><br />|;
 125         print qq| <a href= "/search/pub_search.pl?w9b3_status=pending">See publications pending curation</a><br />|;
 126     } else {
 127         my @curators= CXGN::People::Person::get_curators($dbh);
 128         my %names = map {$_ => CXGN::People::Person->new($dbh, $_)->get_first_name() }  @curators;
 129         my $curator_options=qq|<option value="">--Assign publications to curator--</option>|;
 130         for my $curator_id (keys %names) {
 131             my $curator= $names{$curator_id};
 132             $curator_options .=qq|<option value="$curator_id">$curator</option>|;
 133         }
 134
 135         print <<END_HTML;
 136         <br/>
 137         <form method="post" action="fetch_pubmed.pl">
 138         <table cellpadding="2" cellspacing="2">
 139         <th colspan="2">Curators may use this form to bulk fetch publications from PubMed.<br />&nbsp;</th>
 140         <tr><td><textarea id="" cols="20" rows="10" name="pubmed_ids" value ="Insert a list of  PubMed IDs"></textarea></td>
 141         <td>
 142         <select id="curator_id" name="curator_id"> $curator_options </select>
 143         </td></tr>
 144         <tr><td><input type="submit" name="fetch_pubmeds" value="Store"><input type="reset" value="Reset form" /></td></tr>
 145         </table>
 146         <br />
 147
 148 END_HTML
 149
 150     }
 151     $page->footer();
 152 }
 153 else { $page->client_redirect('/solpeople/login.pl'); }
 154
 155
 156
 157 sub confirm_store {
 158
 159     my $self=shift;
 160     $self->print_confirm_form();
 161 }
 162
 163
 164 sub print_confirm_form {
 165     my $self=shift;
 166     my %args= $self->get_args();
 167
 168     my $query= sanitize_string($args{query});
 169
 170 }
 171
 172