lib/SGN/Controller/AJAX/DocumentBrowser.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::DocumentBrowser - a REST controller class to provide the backend for uploading documents and searching them using the document browser tool.
   5
   6 =head1 DESCRIPTION
   7
   8
   9 =head1 AUTHOR
  10
  11 =cut
  12
  13 package SGN::Controller::AJAX::DocumentBrowser;
  14
  15 use Moose;
  16 use Try::Tiny;
  17 use DateTime;
  18 use File::Slurp;
  19 use File::Spec::Functions;
  20 use File::Copy;
  21 use Data::Dumper;
  22 use CXGN::UploadFile;
  23 use File::Basename qw | basename dirname|;
  24 use JSON;
  25
  26 BEGIN { extends 'Catalyst::Controller::REST' }
  27
  28 __PACKAGE__->config(
  29     default   => 'application/json',
  30     stash_key => 'rest',
  31     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  32    );
  33
  34
  35 sub upload_document :  Path('/ajax/tools/documents/upload') : ActionClass('REST') { }
  36 sub upload_document_POST : Args(0) {
  37     my ($self, $c) = @_;
  38     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  39     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
  40
  41     my $upload = $c->req->upload('upload_document_browser_file_input');
  42     my $upload_original_name = $upload->filename();
  43     my $upload_tempfile = $upload->tempname;
  44     my $time = DateTime->now();
  45     my $timestamp = $time->ymd()."_".$time->hms();
  46
  47     if (!$c->user){
  48         $c->stash->{rest} = { error => 'Must be logged in!' };
  49         $c->detach;
  50     }
  51
  52     my $user_id = $c->user->get_object->get_sp_person_id;
  53     my $user_type = $c->user->get_object->get_user_type();
  54
  55     my $uploader = CXGN::UploadFile->new({
  56         tempfile => $upload_tempfile,
  57         subdirectory => 'document_browser',
  58         archive_path => $c->config->{archive_path},
  59         archive_filename => $upload_original_name,
  60         timestamp => $timestamp,
  61         user_id => $user_id,
  62         user_role => $user_type
  63     });
  64     my $archived_filename_with_path = $uploader->archive();
  65     if (!$archived_filename_with_path){
  66         $c->stash->{rest} = { error => 'Problem archiving the file!' };
  67         $c->detach;
  68     }
  69     my $md5 = $uploader->get_md5($archived_filename_with_path);
  70     if (!$md5){
  71         $c->stash->{rest} = { error => 'Problem retrieving file md5!' };
  72         $c->detach;
  73     }
  74
  75     my $md_row = $metadata_schema->resultset("MdMetadata")->create({create_person_id => $user_id});
  76     $md_row->insert();
  77     my $file_row = $metadata_schema->resultset("MdFiles")
  78         ->create({
  79             basename => basename($archived_filename_with_path),
  80             dirname => dirname($archived_filename_with_path),
  81             filetype => 'document_browser',
  82             md5checksum => $md5->hexdigest(),
  83             metadata_id => $md_row->metadata_id(),
  84         });
  85     $file_row->insert();
  86
  87     $c->stash->{rest} = {success => 'Successfully saved file!'};
  88 }
  89
  90 sub search_document :  Path('/ajax/tools/documents/search') : ActionClass('REST') { }
  91 sub search_document_POST : Args(0) {
  92     my ($self, $c) = @_;
  93     my $file_ids = $c->req->param("file_ids");
  94     my $search = $c->req->param("search");
  95
  96     my $file_ids_ref;
  97     if ($file_ids){
  98         $file_ids_ref = decode_json $file_ids;
  99     }
 100
 101     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 102     my $file_rs = $metadata_schema->resultset("MdFiles")->search({file_id => {-in => $file_ids_ref}});
 103     my @files;
 104     while(my $r = $file_rs->next()){
 105         my $dirname = $r->dirname();
 106         my $basename = $r->basename();
 107         my $file_path = $dirname. "/" .$basename;
 108         push @files, $file_path;
 109     }
 110
 111     my @found_lines;
 112     my @list_elements;
 113     foreach my $f (@files){
 114         open(my $fh, '<', $f)
 115             or die "Could not open file '$f' $!";
 116
 117         while (my $row = <$fh>) {
 118             if (index($row, $search) != -1) {
 119                 push @found_lines, $row;
 120                 my @col = split "\t", $row;
 121                 push @list_elements, $col[0];
 122             }
 123         }
 124     }
 125     $c->stash->{rest} = {success => 1, found_lines => \@found_lines, list_elements => \@list_elements};
 126 }
 127
 128 #########
 129 1;
 130 #########