lib/SGN/Controller/AJAX/PhenotypesUpload.pm

   1
   2 =head1 NAME
   3
   4 SGN::Controller::AJAX::PhenotypesUpload - a REST controller class to provide the
   5 backend for uploading phenotype spreadsheets
   6
   7 =head1 DESCRIPTION
   8
   9 Uploading Phenotype Spreadsheets
  10
  11 =head1 AUTHOR
  12
  13 Jeremy Edwards <jde22@cornell.edu>
  14 Naama Menda <nm249@cornell.edu>
  15 Alex Ogbonna <aco46@cornell.edu>
  16 Nicolas Morales <nm529@cornell.edu>
  17
  18 =cut
  19
  20 package SGN::Controller::AJAX::PhenotypesUpload;
  21
  22 use Moose;
  23 use Try::Tiny;
  24 use DateTime;
  25 use File::Slurp;
  26 use File::Spec::Functions;
  27 use File::Copy;
  28 use Data::Dumper;
  29
  30 BEGIN { extends 'Catalyst::Controller::REST' }
  31
  32 __PACKAGE__->config(
  33     default   => 'application/json',
  34     stash_key => 'rest',
  35     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  36    );
  37
  38
  39 sub upload_phenotype_verify :  Path('/ajax/phenotype/upload_verify') : ActionClass('REST') { }
  40 sub upload_phenotype_verify_POST : Args(1) {
  41     my ($self, $c, $file_type) = @_;
  42     my $store_phenotypes = CXGN::Phenotypes::StorePhenotypes->new();
  43     my $warning_status;
  44
  45     my ($success_status, $error_status, $parsed_data, $plots, $traits, $phenotype_metadata, $timestamp_included, $data_level, $overwrite_values, $image_zip) = _prep_upload($c, $file_type);
  46     if (scalar(@$error_status)>0) {
  47         $c->stash->{rest} = {success => $success_status, error => $error_status };
  48         return;
  49     }
  50
  51     my ($verified_warning, $verified_error) = $store_phenotypes->verify($c, $plots, $traits, $parsed_data, $phenotype_metadata, $timestamp_included, $image_zip);
  52     if ($verified_error) {
  53         push @$error_status, $verified_error;
  54         $c->stash->{rest} = {success => $success_status, error => $error_status };
  55         return;
  56     }
  57     if ($verified_warning) {
  58         push @$warning_status, $verified_warning;
  59     }
  60     push @$success_status, "File data verified. Plot names and trait names are valid.";
  61
  62     $c->stash->{rest} = {success => $success_status, warning => $warning_status, error => $error_status};
  63 }
  64
  65 sub upload_phenotype_store :  Path('/ajax/phenotype/upload_store') : ActionClass('REST') { }
  66 sub upload_phenotype_store_POST : Args(1) {
  67     my ($self, $c, $file_type) = @_;
  68     my $store_phenotypes = CXGN::Phenotypes::StorePhenotypes->new();
  69
  70     my ($success_status, $error_status, $parsed_data, $plots, $traits, $phenotype_metadata, $timestamp_included, $data_level, $overwrite_values, $image_zip) = _prep_upload($c, $file_type);
  71     if (scalar(@$error_status)>0) {
  72         $c->stash->{rest} = {success => $success_status, error => $error_status };
  73         return;
  74     }
  75
  76     #upload_phenotype_store function redoes the same verification that upload_phenotype_verify does before actually uploading. maybe this should be commented out.
  77     #my ($verified_warning, $verified_error) = $store_phenotypes->verify($c,$plots,$traits, $parsed_data, $phenotype_metadata);
  78     #if ($verified_error) {
  79         #push @$error_status, $verified_error;
  80         #$c->stash->{rest} = {success => $success_status, error => $error_status };
  81         #return;
  82     #}
  83     #push @$success_status, "File data verified. Plot names and trait names are valid.";
  84
  85
  86     my $size = scalar(@$plots) * scalar(@$traits);
  87     my $stored_phenotype_error = $store_phenotypes->store($c, $size, $plots, $traits, $parsed_data, $phenotype_metadata, $data_level, $overwrite_values, $image_zip);
  88
  89     if ($stored_phenotype_error) {
  90         push @$error_status, $stored_phenotype_error;
  91         $c->stash->{rest} = {success => $success_status, error => $error_status};
  92         return;
  93     }
  94     push @$success_status, "Metadata saved for archived file.";
  95     push @$success_status, "File data successfully stored.";
  96
  97     $c->stash->{rest} = {success => $success_status, error => $error_status};
  98 }
  99
 100 sub _prep_upload {
 101     my ($c, $file_type) = @_;
 102     my $uploader = CXGN::UploadFile->new();
 103     my $parser = CXGN::Phenotypes::ParseUpload->new();
 104     my @success_status;
 105     my @error_status;
 106     my $timestamp_included;
 107     my $upload;
 108     my $subdirectory;
 109     my $validate_type;
 110     my $metadata_file_type;
 111     my $data_level;
 112     my $image_zip;
 113     if ($file_type eq "spreadsheet") {
 114         print STDERR "Spreadsheet \n";
 115         $subdirectory = "spreadsheet_phenotype_upload";
 116         $validate_type = "phenotype spreadsheet";
 117         $metadata_file_type = "spreadsheet phenotype file";
 118         $timestamp_included = $c->req->param('upload_spreadsheet_phenotype_timestamp_checkbox');
 119         $data_level = $c->req->param('upload_spreadsheet_phenotype_data_level') || 'plots';
 120         $upload = $c->req->upload('upload_spreadsheet_phenotype_file_input');
 121     }
 122     elsif ($file_type eq "fieldbook") {
 123         print STDERR "Fieldbook \n";
 124         $subdirectory = "tablet_phenotype_upload";
 125         $validate_type = "field book";
 126         $metadata_file_type = "tablet phenotype file";
 127         $timestamp_included = 1;
 128         $upload = $c->req->upload('upload_fieldbook_phenotype_file_input');
 129         $image_zip = $c->req->upload('upload_fieldbook_phenotype_images_zipfile');
 130         $data_level = $c->req->param('upload_fieldbook_phenotype_data_level') || 'plots';
 131     }
 132     elsif ($file_type eq "datacollector") {
 133         print STDERR "Datacollector \n";
 134         $subdirectory = "data_collector_phenotype_upload";
 135         $validate_type = "datacollector spreadsheet";
 136         $metadata_file_type = "data collector phenotype file";
 137         $timestamp_included = $c->req->param('upload_datacollector_phenotype_timestamp_checkbox');
 138         $upload = $c->req->upload('upload_datacollector_phenotype_file_input');
 139     }
 140
 141     my $overwrite_values = $c->req->param('phenotype_upload_overwrite_values');
 142     if ($overwrite_values) {
 143         my $user_type = $c->user()->get_object->get_user_type();
 144         print STDERR $user_type."\n";
 145         if ($user_type ne 'curator') {
 146             push @error_status, 'Must be a curator to overwrite values! Please contact us!';
 147         }
 148     }
 149
 150     my $upload_original_name = $upload->filename();
 151     my $upload_tempfile = $upload->tempname;
 152     my %phenotype_metadata;
 153     my $time = DateTime->now();
 154     my $timestamp = $time->ymd()."_".$time->hms();
 155
 156     my $archived_filename_with_path = $uploader->archive($c, $subdirectory, $upload_tempfile, $upload_original_name, $timestamp);
 157     my $md5 = $uploader->get_md5($archived_filename_with_path);
 158     if (!$archived_filename_with_path) {
 159         push @error_status, "Could not save file $upload_original_name in archive.";
 160     } else {
 161         push @success_status, "File $upload_original_name saved in archive.";
 162     }
 163     unlink $upload_tempfile;
 164     #print STDERR "Archived Phenotype File: $archived_filename_with_path\n";
 165
 166     my $archived_image_zipfile_with_path;
 167     if ($image_zip) {
 168         my $upload_original_name = $image_zip->filename();
 169         my $upload_tempfile = $image_zip->tempname;
 170         my %phenotype_metadata;
 171         my $time = DateTime->now();
 172
 173         $archived_image_zipfile_with_path = $uploader->archive($c, $subdirectory, $upload_tempfile, $upload_original_name, $timestamp);
 174         my $md5 = $uploader->get_md5($archived_image_zipfile_with_path);
 175         if (!$archived_image_zipfile_with_path) {
 176             push @error_status, "Could not save images zipfile $upload_original_name in archive.";
 177         } else {
 178             push @success_status, "Images Zip File $upload_original_name saved in archive.";
 179         }
 180         unlink $upload_tempfile;
 181         #print STDERR "Archived Zipfile: $archived_image_zipfile_with_path\n";
 182     }
 183
 184     ## Validate and parse uploaded file
 185     my $validate_file = $parser->validate($validate_type, $archived_filename_with_path, $timestamp_included, $data_level);
 186     if (!$validate_file) {
 187         push @error_status, "Archived file not valid: $upload_original_name.";
 188     }
 189     if ($validate_file == 1){
 190         push @success_status, "File valid: $upload_original_name.";
 191     } else {
 192         if ($validate_file->{'error'}) {
 193             push @error_status, $validate_file->{'error'};
 194         }
 195     }
 196
 197     ## Set metadata
 198     $phenotype_metadata{'archived_file'} = $archived_filename_with_path;
 199     $phenotype_metadata{'archived_file_type'} = $metadata_file_type;
 200     my $operator = $c->user()->get_object()->get_username();
 201     $phenotype_metadata{'operator'} = $operator;
 202     $phenotype_metadata{'date'} = $timestamp;
 203
 204     my $parsed_file = $parser->parse($validate_type, $archived_filename_with_path, $timestamp_included);
 205     if (!$parsed_file) {
 206         push @error_status, "Error parsing file $upload_original_name.";
 207     }
 208     if ($parsed_file->{'error'}) {
 209         push @error_status, $parsed_file->{'error'};
 210     }
 211     my %parsed_data;
 212     my @plots;
 213     my @traits;
 214     if (scalar(@error_status) == 0) {
 215         if ($parsed_file && !$parsed_file->{'error'}) {
 216             %parsed_data = %{$parsed_file->{'data'}};
 217             @plots = @{$parsed_file->{'plots'}};
 218             @traits = @{$parsed_file->{'traits'}};
 219             push @success_status, "File data successfully parsed.";
 220         }
 221     }
 222
 223     return (\@success_status, \@error_status, \%parsed_data, \@plots, \@traits, \%phenotype_metadata, $timestamp_included, $data_level, $overwrite_values, $archived_image_zipfile_with_path);
 224 }
 225
 226 #########
 227 1;
 228 #########