package SGN::View::Mason::Commands; use strict; use vars qw($m $c); HTML::Mason::Component::FileBased->new( 'code' => sub { use utf8; local $SGN::View::Mason::Commands::m = $HTML::Mason::Commands::m; HTML::Mason::Exception::Params->throw ( error => "Odd number of parameters passed to component expecting name/value pairs" ) if @_ % 2; my ( $breeding_programs, $locations, $design_types ); { my %pos; for ( my $x = 0; $x < @_; $x += 2 ) { $pos{ $_[$x] } = $x + 1; } foreach my $arg ( qw( breeding_programs locations ) ) { HTML::Mason::Exception::Params->throw ( error => "no value sent for required parameter '$arg'" ) unless exists $pos{$arg}; } #line 9 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $breeding_programs = $_[ $pos{'breeding_programs'} ]; #line 10 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $locations = $_[ $pos{'locations'} ]; #line 11 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $design_types = exists $pos{'design_types'} ? $_[ $pos{'design_types'} ] : (); } $m->debug_hook( $m->current_comp->path ) if ( HTML::Mason::Compiler::IN_PERL_DB() ); #line 1 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' ' ); #line 13 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' ' ); #line 14 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" my $user_role = ''; my $email_address = ''; if ($c->user) { $user_role = $c->user->get_object()->get_user_type(); $email_address = $c->user->get_object()->get_private_email(); } #line 22 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' ' ); #line 23 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( '/util/import_javascript.mas', classes => [ 'CXGN.TrialTreeFolders' ] ); #line 23 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

Trials may be uploaded in an Excel file (.xls or .xlsx)

' ); #line 617 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( { content => sub { #line 617 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

Header:
The first row (header) must contain the following:

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

Header as a string:

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

' ); #line 646 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" } }, '/page/info_section.mas', title=>"Stock type being evaluated in this trial: accession", collapsible=>1, collapsed=>1 ); #line 646 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' ' ); #line 648 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( { content => sub { #line 648 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

Header:
The first row (header) must contain the following:

plot_name	cross_unique_id	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

Header as a string:

plot_name,cross_unique_id,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

' ); #line 677 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" } }, '/page/info_section.mas', title=>"Stock type being evaluated in this trial: cross unique id", collapsible=>1, collapsed=>1 ); #line 677 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' ' ); #line 679 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( { content => sub { #line 679 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

Header:
The first row (header) must contain the following:

plot_name	family_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

Header as a string:

plot_name,family_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

' ); #line 708 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" } }, '/page/info_section.mas', title=>"Stock type being evaluated in this trial: family name", collapsible=>1, collapsed=>1 ); #line 708 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( ' Required fields:

accession_name or cross_unique_id or family_name (must exist in the database. This is the accession or cross unique id or family name being tested in the plot.)
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.)
block_number (a design parameter indicating which block the plot is in)

Optional fields:

plot_name (must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number}.)
is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions/cross unique ids/family names that are controls, so you should indicate the plots of those accessions/cross unique ids/family names as a control.)
rep_number (replicate number, numeric)
range_number (range number. often synonymous with col_number, numeric)
row_number (row number. If the field is a grid, this represents the y coordinate, numeric, required for field map generation.)
col_number (column number. If the field is a grid, this represents the x coordinate. Sometimes called range_number, numeric, required for field map generation.)
seedlot_name (the seedlot from where the planted seed originated. Must exist in the database)
num_seed_per_plot (number seeds per plot. Seed is transferred from seedlot mentioned in seedlot_name. Numeric)
weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. Numeric)
entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). The value for each plot should be 1 if the treatment was applied or empty.)

Only the required fields are necessary to include in the upload template. You may add any additional optional fields. The fields can be in any order.

Multiple Trial Designs:
Header:
The first row (header) must contain the following, which is an expansion of the single trial design header:

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

Header as a string:

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

Required fields:

trial_name (Must be unique across entire database. It is often a concatenation of the year, transplanting_date, purpose, unique number, and location.)
breeding_program (The name of breeding program that managed the trial, must exist in the database.)
location (The name or abbreviation of the location where the trial was held, must exist in the database.)
year (The year the trial was held.)
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), URDD (Un-Replicated Diagonal Design), 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))
description (Additional text with any other relevant information about the trial.)
accession_name OR cross_unique_id OR family_name (The accession, cross, or family being tested in the plot, must exist in the database.)
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.)
block_number (A design parameter indicating which block the plot is in.)

Additional optional fields:

plot_name (Must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number})
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)
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)
plot_width (plot width in meters)
plot_length (plot length in meters)
field_size (field size in hectares)
planting_date (Date of Planting in YYYY-MM-DD format)
transplanting_date(The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format)
harvest_date (Date of Harvest in YYYY-MM-DD format)
is_a_control (type 1 in this field if the plot is a control, otherwise 0 or leave blank. generally you will have accessions that are controls, so you should indicate the plots that that accession is in as a control.)
rep_number (replicate number, must be numeric)
range_number (range number. often synonymous with col_number, must be numeric)
row_number (row number. if the field is a grid, this represents the y coordinate, numeric, required for field map generation.)
col_number (column number. if the field is a grid, this represents the x coordinate. sometimes called range_number, numeric, required for field map generation.)
seedlot_name (the seedlot from where the planted seed originated. must exist in the database)
num_seed_per_plot (number seeds per plot. seed is transferred from seedlot mentioned in seedlot_name. numeric)
weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. numeric)
entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). the value for each plot should be 1 if the treatment was applied or empty if not applied.)

' ); #line 845 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( '/help/file_upload_type.mas', type => "Trials", optional_column => 1 ); #line 845 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

Header:
The first row (header) should contain the following:

trial_name	breeding_program	location	year	transplanting_date	planting_date	harvest_date	design_type	description	trial_type	plot_width	plot_length	field_size

Required Fields:

trial_name: the name of the trial (must already exist in the database)

Optional values:

new_trial_name (A new name for the trial, must not already exist in the database)
breeding_program (The name of breeding program that managed the trial, must exist in the database.)
location (The name or abbreviation of the location where the trial was held, must exist in the database.)
year (The year the trial was held.)
transplanting_date (The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format or \'remove\' to remove the date)
planting_date (Date of Planting in YYYY-MM-DD format or \'remove\' to remove the date)
harvest_date (Date of Harvest in YYYY-MM-DD format or \'remove\' to remove the date)
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), URDD (Un-Replicated Diagonal Design), 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), p-rep (Partially Replicated), Westcott (Westcott Design))
description (Additional text with any other relevant information about the trial.)
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)
plot_width (plot width in meters)
plot_length (plot length in meters)
field_size (field size in hectares)

' ); #line 956 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->comp( '/help/file_upload_type.mas', type => "Trial Metadata", optional_column => 1 ); #line 956 "/home/production/cxgn/sgn/mason/breeders_toolbox/trial/trial_upload_dialogs.mas" $m->print( '

' ); ;return; }, 'declared_args' => { '$breeding_programs' => { default => undef }, '$design_types' => { default => ' ()' }, '$locations' => { default => undef } }, 'load_time' => 1763079527, ) ;

Number of rows per plot
Number of columns per plot