Multi-Trial Upload: allow crosses

bin/upload_multiple_trial_design.pl

@@ -145,6 +145,7 @@ =head1 AUTHOR
             trial_location => $trial_design->{'location'},
             trial_name => $trial_name,
             design_type => $trial_design->{'design_type'},
+            trial_stock_type => $trial_design->{'trial_stock_type'},
             design => $trial_design->{'design_details'},
             program => $trial_design->{'breeding_program'},
             upload_trial_file => $infile,

lib/CXGN/Trial/ParseUpload/Plugin/MultipleTrialDesignGeneric.pm

@@ -10,7 +10,7 @@ use CXGN::Calendar;
 use CXGN::Trial;
 
 my @REQUIRED_COLUMNS = qw|trial_name breeding_program location year design_type description accession_name plot_number block_number|;
-my @OPTIONAL_COLUMNS = qw|plot_name trial_type plot_width plot_length field_size planting_date transplanting_date harvest_date is_a_control rep_number range_number row_number col_number seedlot_name num_seed_per_plot weight_gram_seed_per_plot entry_number|;
+my @OPTIONAL_COLUMNS = qw|plot_name trial_type trial_stock_type plot_width plot_length field_size planting_date transplanting_date harvest_date is_a_control rep_number range_number row_number col_number seedlot_name num_seed_per_plot weight_gram_seed_per_plot entry_number|;
 # Any additional columns that are not required or optional will be used as a treatment
 
 # VALID DESIGN TYPES
@@ -33,6 +33,13 @@ my %valid_design_types = (
     "Analysis" => 1
 );
 
+# VALID STOCK TYPES
+my %valid_stock_types = (
+    "accession" => 1,
+    "cross" => 1,
+    "family_name" => 1
+);
+
 sub _validate_with_plugin {
     my $self = shift;
     my $filename = $self->get_filename();
@@ -56,7 +63,10 @@ sub _validate_with_plugin {
     my $parser = CXGN::File::Parse->new(
         file => $filename,
         required_columns => \@REQUIRED_COLUMNS,
-        optional_columns => \@OPTIONAL_COLUMNS
+        optional_columns => \@OPTIONAL_COLUMNS,
+        column_aliases => {
+            'accession_name' => [ 'stock_name', 'cross_unique_id', 'family_name' ]
+        }
     );
     my $parsed = $parser->parse();
     my $parsed_errors = $parsed->{'errors'};
@@ -339,9 +349,17 @@ sub _validate_with_plugin {
         }
     }
 
+    # Trial Stock Type: must be a valid / supported trial stock type
+    foreach (@{$parsed_values->{'trial_stock_type'}}) {
+        if ( !exists $valid_stock_types{$_} ) {
+            push @error_messages, "trial_stock_type <strong>$_</strong> is not supported. Supported trial stock types: " . join(', ', keys(%valid_stock_types)) . ".";
+        }
+    }
+
     # Accession Names: must exist in the database
     my @accessions = @{$parsed_values->{'accession_name'}};
     my $accessions_hashref = $validator->validate($schema,'accessions',\@accessions);
+    my @multiple_synonyms = @{$accessions_hashref->{'multiple_synonyms'}};
 
     #find unique synonyms. Sometimes trial uploads use synonym names instead of the unique accession name. We allow this if the synonym is unique and matches one accession in the database
     my @synonyms = @{$accessions_hashref->{'synonyms'}};
@@ -356,12 +374,11 @@ sub _validate_with_plugin {
     }
 
     #now validate again the accession names
-    $accessions_hashref = $validator->validate($schema,'accessions',\@accessions);
+    $accessions_hashref = $validator->validate($schema,'accessions_or_crosses_or_familynames',\@accessions);
     my @accessions_missing = @{$accessions_hashref->{'missing'}};
-    my @multiple_synonyms = @{$accessions_hashref->{'multiple_synonyms'}};
 
     if (scalar(@accessions_missing) > 0) {
-        push @error_messages, "Accession(s) <strong>".join(',',@accessions_missing)."</strong> are not in the database as uniquenames or synonyms.";
+        push @error_messages, "Stocks(s) <strong>".join(',',@accessions_missing)."</strong> are not in the database as uniquenames or synonyms of accessions, crosses, or families.";
     }
     if (scalar(@multiple_synonyms) > 0) {
         my @msgs;
@@ -554,6 +571,7 @@ sub _parse_with_plugin {
             $single_design{'year'} = $row->{'year'};
             $single_design{'design_type'} = $row->{'design_type'};
             $single_design{'description'} = $row->{'description'};
+            $single_design{'trial_stock_type'} = $row->{'trial_stock_type'} || 'accession';
             $single_design{'plot_width'} = $row->{'plot_width'};
             $single_design{'plot_length'} = $row->{'plot_length'};
             $single_design{'field_size'} = $row->{'field_size'};

mason/breeders_toolbox/trial/trial_upload_dialogs.mas

@@ -746,6 +746,7 @@ $design_types => ()
                                 <td>design_type</td>
                                 <td>description</td>
                                 <td>trial_type</td>
+                                <td>trial_stock_type</td>
                                 <td>plot_width</td>
                                 <td>plot_length</td>
                                 <td>field_size</td>
@@ -769,7 +770,7 @@ $design_types => ()
                     </table>
 
                     <b>Header as a string:</b><br/>
-                    <p>trial_name,breeding_program,location,year,transplanting_date,design_type,description,trial_type,plot_width,plot_length,field_size,planting_date,harvest_date,plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot,entry_number</p>
+                    <p>trial_name,breeding_program,location,year,transplanting_date,design_type,description,trial_type,trial_stock_type,plot_width,plot_length,field_size,planting_date,harvest_date,plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot,entry_number</p>
 
                     <b> Required fields:</b>
                     <ul>
@@ -780,7 +781,7 @@ $design_types => ()
 
                     <li>design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), stripplot (Strip Plot / Split Block), p-rep (Partially Replicated), Westcott (Westcott Design))</li>
                     <li>description (Additional text with any other relevant information about the trial.)</li>
-                    <li>accession_name (The accession being tested in the plot, must exist in the database.)</li>
+                    <li>accession_name OR cross_unique_id OR family_name (The accession, cross, or family being tested in the plot, must exist in the database.)</li>
                     <li>plot_number (A sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.)</li>
                     <li>block_number (A design parameter indicating which block the plot is in.)</li>
                     </ul>
@@ -789,6 +790,7 @@ $design_types => ()
                     <ul>
                     <li>plot_name (Must be unique across entire database. If not provided in the file, it will be automatically generated as <code>{trial_name}-PLOT_{plot_number}</code>)</li>
                     <li>trial_type (The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial)</li>
+                    <li>trial_stock_type (The type of stocks that are being evaluated in the trial.  Can be either 'accession', 'cross', or 'family_name'.  When not provided, 'accession' is used as the default)
                     <li>plot_width (plot width in meters)</li>
                     <li>plot_length (plot length in meters)</li>
                     <li>field_size (field size in hectares)</li>

t/selenium2/breeders/upload_multi_trial_file.t

@@ -156,7 +156,8 @@ for my $extension ("xlsx", "xls", "csv") {
             'trial_type'       => 76515,
             'breeding_program' => 'test',
             'plot_width'       => '5',
-            'field_size'       => '8'
+            'field_size'       => '8',
+            'trial_stock_type' => 'accession'
         },
         '199275HBEPR_stom' => {
             'breeding_program' => 'test',
@@ -227,7 +228,8 @@ for my $extension ("xlsx", "xls", "csv") {
             'year'          => '1999',
             'planting_date' => '1992-09-19',
             'plot_length'   => '5',
-            'design_type'   => 'Augmented'
+            'design_type'   => 'Augmented',
+            'trial_stock_type' => 'accession'
         },
         '199934HBEPR_cara' => {
             'description'    => 'EPR',
@@ -298,7 +300,8 @@ for my $extension ("xlsx", "xls", "csv") {
             'design_type'      => 'Augmented',
             'plot_length'      => '5',
             'harvest_date'     => '2000-03-14',
-            'year'             => '1999'
+            'year'             => '1999',
+            'trial_stock_type' => 'accession'
         },
         '199947HBEPR_mora' => {
             'year'         => '1999',
@@ -369,7 +372,8 @@ for my $extension ("xlsx", "xls", "csv") {
             },
             'location'    => 'test_location',
             'trial_type'  => 76515,
-            'description' => 'EPR'
+            'description' => 'EPR',
+            'trial_stock_type' => 'accession'
         }
     };