From a048340dc7b16df07e1223aa8915dd6a15041997 Mon Sep 17 00:00:00 2001 From: titima15 Date: Wed, 11 Feb 2026 10:28:44 -0500 Subject: [PATCH 1/9] seedlot inventory upload generic --- .../Plugin/SeedlotInventoryGeneric.pm | 138 ++++++++++++++++++ 1 file changed, 138 insertions(+) create mode 100644 lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm new file mode 100644 index 0000000000..f4bf6268bb --- /dev/null +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm @@ -0,0 +1,138 @@ +package CXGN::Stock::Seedlot::ParseUpload::Plugin::SeedlotInventoryGeneric; + +use Moose::Role; +use CXGN::File::Parse; +use CXGN::Stock::StockLookup; +use SGN::Model::Cvterm; +use Data::Dumper; +use CXGN::List::Validate; + +sub _validate_with_plugin { + my $self = shift; + + my $filename = $self->get_filename(); + my $schema = $self->get_chado_schema(); + + my @error_messages; + my %errors; + my %missing_seedlots; + + my $parser = CXGN::File::Parse->new ( + file => $filename, + required_columns => [ 'box_id', 'seed_id', 'inventory_date', 'inventory_person'], + optional_columns => ['weight_gram', 'amount'], + column_aliases => { + 'box_id' => ['box id', 'box name', box_name], + 'seed_id' => ['seed id', 'seedlot_name', 'seedlot name'], + 'inventory_date' => ['inventory date'], + 'inventory_person' => ['inventory person'], + 'weight_gram' => ['weight(g)', 'weight gram'], + }, + ); + + my $parsed = $parser->parse(); + my $parsed_errors = $parsed->{errors}; + my $parsed_columns = $parsed->{columns}; + my $parsed_data = $parsed->{data}; + my $parsed_values = $parsed->{values}; + my $additional_columns = $parsed->{additional_columns}; + + if ( $parsed_errors && scalar(@$parsed_errors) > 0 ) { + $errors{'error_messages'} = $parsed_errors; + $self->_set_parse_errors(\%errors); + return; + } + + if ( $additional_columns && scalar(@$additional_columns) > 0 ) { + $errors{'error_messages'} = [ + "The following columns are not recognized: " . join(', ', @$additional_columns) . ". Please check the spreadsheet format for the allowed columns." + ]; + $self->_set_parse_errors(\%errors); + return; + } + + for my $row ( @$parsed_data ) { + my $row_num = $row->{_row}; + my $seedlot_name = $row->{'seedlot_id'}; + my $amount = $row->{'amount'}; + my $weight = $row->{'weight_gram'}; + + if ( (!$amount || $amount eq '') && (!$weight || $weight eq '')) { + push @error_messages, "On row:$row_num you must provide either a weight in grams or a seed count amount."; + } + } + + my $seen_seedlot_names = $parsed_values->{'seedlot_id'}; + + my $seedlot_validator = CXGN::List::Validate->new(); + my @seedlots_missing = @{$seedlot_validator->validate($schema,'seedlots',$seen_seedlot_names)->{'missing'}}; + + if (scalar(@seedlots_missing) > 0) { + push @error_messages, "The following seedlots are not in the database as uniquenames: ".join(',',@seedlots_missing); + } + + if (scalar(@error_messages) >= 1) { + $errors{'error_messages'} = \@error_messages; + $self->_set_parse_errors(\%errors); + return; + } else { + $self->_set_parsed_data($parsed); + } + + return 1; + +} + +sub _parse_with_plugin { + my $self = shift; + my $schema = $self->get_chado_schema(); + my $parsed = $self->_parsed_data(); + my $parsed_data = $parsed->{data}; + my $parsed_values = $parsed->{values}; + my %parsed_result; + my %seen_seedlot_names; + + my $accession_names = $parsed_values->{'accession_name'}; + my $seedlot_names = $parsed_values->{'seedlot_name'}; + + for my $row (@$parsed_data) { + my $row_num; + my $seed_id; + my $box_id; + my $inventory_date; + my $inventory_person; + my $weight_gram; + my $amount; + $seen_seedlot_names{$seed_id}++; + + $row_num = $row->{_row}; + $seed_id = $row->{'seed_id'}; + $box_id = $row->{'box_id'}; + $inventory_date = $row->{'inventory_date'}; + $inventory_person = $row->{'inventory_person'}; + $weight_gram = $row->{'weight_gram'}; + $amount = $row->{'amount'}; + + $parse_result{$seed_id} = { + box_id => $box_id, + seedlot_name => $seed_id, + inventory_date => $inventory_date, + inventory_person => $inventory_person, + weight_gram => $weight_gram + }; + } + + my @seedlot_names = keys %seen_seedlot_names; + my $seedlots_rs = $schema->resultset("Stock::Stock")->search({uniquename => {-in => \@seedlot_names}}); + while (my $r = $seedlots_rs->next){ + $parse_result{$r->uniquename}->{seedlot_id} = $r->stock_id; + } + + $self->_set_parsed_data(\%parsed_result); + + return 1; + +} + + +1; From 46ff8fd7bbcf7d4a8d3b0f57496454ae88d836f2 Mon Sep 17 00:00:00 2001 From: titima15 Date: Wed, 11 Feb 2026 10:53:28 -0500 Subject: [PATCH 2/9] option to use amount for seedlot inventory --- lib/SGN/Controller/AJAX/Seedlot.pm | 52 +++++++++++++++++++----------- 1 file changed, 33 insertions(+), 19 deletions(-) diff --git a/lib/SGN/Controller/AJAX/Seedlot.pm b/lib/SGN/Controller/AJAX/Seedlot.pm index f5c73f0dfe..90e2fc6b25 100644 --- a/lib/SGN/Controller/AJAX/Seedlot.pm +++ b/lib/SGN/Controller/AJAX/Seedlot.pm @@ -912,41 +912,55 @@ sub upload_seedlots_inventory_POST : Args(0) { while (my ($key, $val) = each(%$parsed_data)){ my $sl = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $val->{seedlot_id}); $sl->box_name($val->{box_id}); - $sl->description($val->{description}); +# $sl->description($val->{description}); - print STDERR "QUALITY: $val->{quality}\n"; - $sl->quality($val->{quality}); +# print STDERR "QUALITY: $val->{quality}\n"; +# $sl->quality($val->{quality}); my $return = $sl->store(); - my $current_stored_count = $sl->get_current_count_property(); + my $current_stored_count = $sl->get_current_count_property(); my $current_stored_weight = $sl->get_current_weight_property(); - - my $weight_difference = $val->{weight_gram} - $current_stored_weight; + my $weight_difference; + my $amount_difference; my $factor; - if ($weight_difference >= 0){ - $factor = 1; - } else { - $factor = -1; - $weight_difference = $weight_difference * -1; #Store positive values only + if ($val->{weight_gram}) { + $weight_difference = $val->{weight_gram} - $current_stored_weight; + if ($weight_difference >= 0){ + $factor = 1; + } else { + $factor = -1; + $weight_difference = $weight_difference * -1; #Store positive values only + } + } + + if ($val->{amount}) { + $amount_difference = $val->{amount} - $current_stored_count; + if ($amount_difference >= 0){ + $factor = 1; + } else { + $factor = -1; + $amount_difference = $amount_difference * -1; #Store positive values only + } } my $transaction = CXGN::Stock::Seedlot::Transaction->new(schema => $schema); $transaction->factor($factor); - my $from_stock_id = $val->{seedlot_id}; - my $from_stock_name = $val->{seedlot_name}; +# my $from_stock_id = $val->{seedlot_id}; +# my $from_stock_name = $val->{seedlot_name}; - if ($val->{source_id}) { - $from_stock_id = $val->{source_id}; - $from_stock_name = $val->{source}; - } +# if ($val->{source_id}) { +# $from_stock_id = $val->{source_id}; +# $from_stock_name = $val->{source}; +# } - $transaction->from_stock([ $from_stock_id, $from_stock_name ]); +# $transaction->from_stock([ $from_stock_id, $from_stock_name ]); $transaction->to_stock([$val->{seedlot_id}, $val->{seedlot_name}]); $transaction->weight_gram($weight_difference); + $transaction->amount($amount_difference); $transaction->timestamp($val->{inventory_date}); - $transaction->description('Seed inventory CSV upload.'); + $transaction->description('Seed inventory upload.'); $transaction->operator($val->{inventory_person}); $transaction->store(); From 43300bb01b292979d06a99540a90de9c74acbc49 Mon Sep 17 00:00:00 2001 From: titima15 Date: Wed, 11 Feb 2026 14:35:20 -0500 Subject: [PATCH 3/9] fix plugin --- .../Plugin/SeedlotInventoryGeneric.pm | 33 +++++++++++++------ lib/SGN/Controller/AJAX/Seedlot.pm | 32 +++++++----------- 2 files changed, 35 insertions(+), 30 deletions(-) diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm index f4bf6268bb..d310323435 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm @@ -22,11 +22,13 @@ sub _validate_with_plugin { required_columns => [ 'box_id', 'seed_id', 'inventory_date', 'inventory_person'], optional_columns => ['weight_gram', 'amount'], column_aliases => { - 'box_id' => ['box id', 'box name', box_name], + 'box_id' => ['box id', 'box name', 'box_name'], 'seed_id' => ['seed id', 'seedlot_name', 'seedlot name'], 'inventory_date' => ['inventory date'], 'inventory_person' => ['inventory person'], 'weight_gram' => ['weight(g)', 'weight gram'], + 'amount' => ['count'], + }, ); @@ -57,7 +59,12 @@ sub _validate_with_plugin { my $amount = $row->{'amount'}; my $weight = $row->{'weight_gram'}; - if ( (!$amount || $amount eq '') && (!$weight || $weight eq '')) { + if (!$amount || $amount eq '') { + $amount = 'NA'; + } elsif (!$weight || $weight eq '') { + $weight = 'NA'; + } + if ($amount eq 'NA' && $weight eq 'NA') { push @error_messages, "On row:$row_num you must provide either a weight in grams or a seed count amount."; } } @@ -101,33 +108,39 @@ sub _parse_with_plugin { my $box_id; my $inventory_date; my $inventory_person; - my $weight_gram; + my $weight; my $amount; - $seen_seedlot_names{$seed_id}++; - $row_num = $row->{_row}; $seed_id = $row->{'seed_id'}; $box_id = $row->{'box_id'}; $inventory_date = $row->{'inventory_date'}; $inventory_person = $row->{'inventory_person'}; - $weight_gram = $row->{'weight_gram'}; + $weight = $row->{'weight_gram'}; $amount = $row->{'amount'}; + $seen_seedlot_names{$seed_id}++; + + if (!$amount || $amount eq '') { + $amount = 'NA'; + } elsif (!$weight || $weight eq '') { + $weight = 'NA'; + } - $parse_result{$seed_id} = { + $parsed_result{$seed_id} = { box_id => $box_id, seedlot_name => $seed_id, inventory_date => $inventory_date, inventory_person => $inventory_person, - weight_gram => $weight_gram + weight_gram => $weight, + amount => $amount }; } my @seedlot_names = keys %seen_seedlot_names; my $seedlots_rs = $schema->resultset("Stock::Stock")->search({uniquename => {-in => \@seedlot_names}}); while (my $r = $seedlots_rs->next){ - $parse_result{$r->uniquename}->{seedlot_id} = $r->stock_id; + $parsed_result{$r->uniquename}{seedlot_id} = $r->stock_id; } - + print STDERR "PARSED RESULT PLUGIN =".Dumper(\%parsed_result)."\n"; $self->_set_parsed_data(\%parsed_result); return 1; diff --git a/lib/SGN/Controller/AJAX/Seedlot.pm b/lib/SGN/Controller/AJAX/Seedlot.pm index 90e2fc6b25..ce78240a2c 100644 --- a/lib/SGN/Controller/AJAX/Seedlot.pm +++ b/lib/SGN/Controller/AJAX/Seedlot.pm @@ -887,7 +887,7 @@ sub upload_seedlots_inventory_POST : Args(0) { } unlink $upload_tempfile; my $parser = CXGN::Stock::Seedlot::ParseUpload->new(chado_schema => $schema, filename => $archived_filename_with_path); - $parser->load_plugin('SeedlotInventoryCSV'); + $parser->load_plugin('SeedlotInventoryGeneric'); my $parsed_data = $parser->parse(); #print STDERR Dumper $parsed_data; @@ -907,16 +907,11 @@ sub upload_seedlots_inventory_POST : Args(0) { $c->stash->{rest} = {error_string => $return_error, missing_seedlots => $parse_errors->{'missing_seedlots'} }; $c->detach(); } - + print STDERR "PARSED DATA =".Dumper($parsed_data)."\n"; eval { while (my ($key, $val) = each(%$parsed_data)){ my $sl = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $val->{seedlot_id}); $sl->box_name($val->{box_id}); -# $sl->description($val->{description}); - -# print STDERR "QUALITY: $val->{quality}\n"; -# $sl->quality($val->{quality}); - my $return = $sl->store(); my $current_stored_count = $sl->get_current_count_property(); @@ -924,8 +919,11 @@ sub upload_seedlots_inventory_POST : Args(0) { my $weight_difference; my $amount_difference; my $factor; - if ($val->{weight_gram}) { - $weight_difference = $val->{weight_gram} - $current_stored_weight; + my $inventory_weight = $val->{weight_gram}; + my $inventory_amount = $val->{amount}; + + if (defined $inventory_weight) { + $weight_difference = $inventory_weight - $current_stored_weight; if ($weight_difference >= 0){ $factor = 1; } else { @@ -934,8 +932,8 @@ sub upload_seedlots_inventory_POST : Args(0) { } } - if ($val->{amount}) { - $amount_difference = $val->{amount} - $current_stored_count; + if (defined $inventory_amount) { + $amount_difference = $inventory_amount - $current_stored_count; if ($amount_difference >= 0){ $factor = 1; } else { @@ -947,15 +945,9 @@ sub upload_seedlots_inventory_POST : Args(0) { my $transaction = CXGN::Stock::Seedlot::Transaction->new(schema => $schema); $transaction->factor($factor); -# my $from_stock_id = $val->{seedlot_id}; -# my $from_stock_name = $val->{seedlot_name}; - -# if ($val->{source_id}) { -# $from_stock_id = $val->{source_id}; -# $from_stock_name = $val->{source}; -# } - -# $transaction->from_stock([ $from_stock_id, $from_stock_name ]); + my $from_stock_id = $val->{seedlot_id}; + my $from_stock_name = $val->{seedlot_name}; + $transaction->from_stock([ $from_stock_id, $from_stock_name ]); $transaction->to_stock([$val->{seedlot_id}, $val->{seedlot_name}]); $transaction->weight_gram($weight_difference); $transaction->amount($amount_difference); From 269e1f8af49e35db6930641d0204b9d06bb4d6a5 Mon Sep 17 00:00:00 2001 From: titima15 Date: Wed, 11 Feb 2026 16:18:33 -0500 Subject: [PATCH 4/9] explicitly indicate amount or weight --- .../Seedlot/ParseUpload/Plugin/SeedlotInventoryCSV.pm | 5 +++++ .../ParseUpload/Plugin/SeedlotInventoryGeneric.pm | 2 +- lib/SGN/Controller/AJAX/Seedlot.pm | 11 +++++++---- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryCSV.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryCSV.pm index f023a8d4b9..8614883fb5 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryCSV.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryCSV.pm @@ -6,6 +6,11 @@ use Data::Dumper; use Text::CSV; use CXGN::List::Validate; +# +# DEPRECATED: This plugin has been replaced by the SeedlotInventoryGeneric plugin +# + + sub _validate_with_plugin { my $self = shift; my $filename = $self->get_filename(); diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm index d310323435..2fc480b014 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm @@ -140,7 +140,7 @@ sub _parse_with_plugin { while (my $r = $seedlots_rs->next){ $parsed_result{$r->uniquename}{seedlot_id} = $r->stock_id; } - print STDERR "PARSED RESULT PLUGIN =".Dumper(\%parsed_result)."\n"; + $self->_set_parsed_data(\%parsed_result); return 1; diff --git a/lib/SGN/Controller/AJAX/Seedlot.pm b/lib/SGN/Controller/AJAX/Seedlot.pm index ce78240a2c..21419a76de 100644 --- a/lib/SGN/Controller/AJAX/Seedlot.pm +++ b/lib/SGN/Controller/AJAX/Seedlot.pm @@ -922,7 +922,7 @@ sub upload_seedlots_inventory_POST : Args(0) { my $inventory_weight = $val->{weight_gram}; my $inventory_amount = $val->{amount}; - if (defined $inventory_weight) { + if ($inventory_weight ne 'NA') { $weight_difference = $inventory_weight - $current_stored_weight; if ($weight_difference >= 0){ $factor = 1; @@ -932,7 +932,7 @@ sub upload_seedlots_inventory_POST : Args(0) { } } - if (defined $inventory_amount) { + if ($inventory_amount ne 'NA') { $amount_difference = $inventory_amount - $current_stored_count; if ($amount_difference >= 0){ $factor = 1; @@ -949,8 +949,11 @@ sub upload_seedlots_inventory_POST : Args(0) { my $from_stock_name = $val->{seedlot_name}; $transaction->from_stock([ $from_stock_id, $from_stock_name ]); $transaction->to_stock([$val->{seedlot_id}, $val->{seedlot_name}]); - $transaction->weight_gram($weight_difference); - $transaction->amount($amount_difference); + if ($inventory_weight ne 'NA') { + $transaction->weight_gram($weight_difference); + } elsif ($inventory_amount ne 'NA') { + $transaction->amount($amount_difference); + } $transaction->timestamp($val->{inventory_date}); $transaction->description('Seed inventory upload.'); $transaction->operator($val->{inventory_person}); From 1ccb0368f2ff89aae469e1a258dc903d4d8d59f8 Mon Sep 17 00:00:00 2001 From: titima15 Date: Wed, 11 Feb 2026 16:56:49 -0500 Subject: [PATCH 5/9] modify spreadsheet info --- .../upload_seedlots_inventory_dialogs.mas | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/mason/breeders_toolbox/upload_seedlots_inventory_dialogs.mas b/mason/breeders_toolbox/upload_seedlots_inventory_dialogs.mas index 9403f576b3..fc61e955aa 100644 --- a/mason/breeders_toolbox/upload_seedlots_inventory_dialogs.mas +++ b/mason/breeders_toolbox/upload_seedlots_inventory_dialogs.mas @@ -154,10 +154,6 @@
- Seedlots may be uploaded in a CSV file (.csv) -
- (Excel .xls and .xlsx format not supported) -

Header:
The first row (header) should contain the following: @@ -175,17 +171,23 @@ - + Note: If you would like to upload number of materials in seedlot instead of weight, you can replace the header 'weight_gram' with 'amount' +
+
Required fields:
  • box_id (the name of the box that the seedlot is in. also called box_name.)
  • seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)
  • inventory_date (a timestamp for when the seedlot was inventoried)
  • inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)
    • -
  • weight_gram (the weight in grams of the seedlot)
    • +
  • weight_gram (the weight in grams of the seedlot) +
    OR
    + amount (number of materials in seedlot.)
    • +
+ <& /help/file_upload_type.mas, type => "Seedlot Inventory", optional_column => 0 &>
From 603658ca07c5be5b5cf3fa62f37ddaa1eb0f166d Mon Sep 17 00:00:00 2001 From: titima15 Date: Thu, 12 Feb 2026 10:33:10 -0500 Subject: [PATCH 6/9] modify plugin --- .../ParseUpload/Plugin/SeedlotInventoryGeneric.pm | 15 ++------------- lib/SGN/Controller/AJAX/Seedlot.pm | 9 ++++----- 2 files changed, 6 insertions(+), 18 deletions(-) diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm index 2fc480b014..bd6819f092 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm @@ -59,12 +59,7 @@ sub _validate_with_plugin { my $amount = $row->{'amount'}; my $weight = $row->{'weight_gram'}; - if (!$amount || $amount eq '') { - $amount = 'NA'; - } elsif (!$weight || $weight eq '') { - $weight = 'NA'; - } - if ($amount eq 'NA' && $weight eq 'NA') { + if (!defined $amount && !defined $weight) { push @error_messages, "On row:$row_num you must provide either a weight in grams or a seed count amount."; } } @@ -119,12 +114,6 @@ sub _parse_with_plugin { $amount = $row->{'amount'}; $seen_seedlot_names{$seed_id}++; - if (!$amount || $amount eq '') { - $amount = 'NA'; - } elsif (!$weight || $weight eq '') { - $weight = 'NA'; - } - $parsed_result{$seed_id} = { box_id => $box_id, seedlot_name => $seed_id, @@ -140,7 +129,7 @@ sub _parse_with_plugin { while (my $r = $seedlots_rs->next){ $parsed_result{$r->uniquename}{seedlot_id} = $r->stock_id; } - + $self->_set_parsed_data(\%parsed_result); return 1; diff --git a/lib/SGN/Controller/AJAX/Seedlot.pm b/lib/SGN/Controller/AJAX/Seedlot.pm index 21419a76de..cd71bbd893 100644 --- a/lib/SGN/Controller/AJAX/Seedlot.pm +++ b/lib/SGN/Controller/AJAX/Seedlot.pm @@ -907,7 +907,6 @@ sub upload_seedlots_inventory_POST : Args(0) { $c->stash->{rest} = {error_string => $return_error, missing_seedlots => $parse_errors->{'missing_seedlots'} }; $c->detach(); } - print STDERR "PARSED DATA =".Dumper($parsed_data)."\n"; eval { while (my ($key, $val) = each(%$parsed_data)){ my $sl = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $val->{seedlot_id}); @@ -922,7 +921,7 @@ sub upload_seedlots_inventory_POST : Args(0) { my $inventory_weight = $val->{weight_gram}; my $inventory_amount = $val->{amount}; - if ($inventory_weight ne 'NA') { + if (defined $inventory_weight) { $weight_difference = $inventory_weight - $current_stored_weight; if ($weight_difference >= 0){ $factor = 1; @@ -932,7 +931,7 @@ sub upload_seedlots_inventory_POST : Args(0) { } } - if ($inventory_amount ne 'NA') { + if (defined $inventory_amount) { $amount_difference = $inventory_amount - $current_stored_count; if ($amount_difference >= 0){ $factor = 1; @@ -949,9 +948,9 @@ sub upload_seedlots_inventory_POST : Args(0) { my $from_stock_name = $val->{seedlot_name}; $transaction->from_stock([ $from_stock_id, $from_stock_name ]); $transaction->to_stock([$val->{seedlot_id}, $val->{seedlot_name}]); - if ($inventory_weight ne 'NA') { + if (defined $inventory_weight) { $transaction->weight_gram($weight_difference); - } elsif ($inventory_amount ne 'NA') { + } elsif (defined $inventory_amount) { $transaction->amount($amount_difference); } $transaction->timestamp($val->{inventory_date}); From 38d7ea0a7db9a0e045f8cc76a958f18e2338bb40 Mon Sep 17 00:00:00 2001 From: titima15 Date: Thu, 12 Feb 2026 14:53:49 -0500 Subject: [PATCH 7/9] tests --- t/data/stock/seedlot_inventory_amount.xlsx | Bin 0 -> 5090 bytes t/unit_mech/AJAX/Stocks/UploadSeedlots.t | 51 +++++++++++++++++++-- 2 files changed, 48 insertions(+), 3 deletions(-) create mode 100644 t/data/stock/seedlot_inventory_amount.xlsx diff --git a/t/data/stock/seedlot_inventory_amount.xlsx b/t/data/stock/seedlot_inventory_amount.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..500646fec7b99f68522ad2eb0de44be84ef9dd7d GIT binary patch literal 5090 zcmaJ_by!sIwjR3Ep=;~@$9FXotK)Oqj5Cmx?q(>U05k?6~X$fh# zgTHf+T+cnO{XBd2AA5a!zO~-(UGG{D6%0%u02db*(3GZX2)JehsAm(nmA$i|z}3Ap z{*!Ho5MkK15B_Vfh3XLD`wHi)6o(ede(Z zsCWbwcnZ7BRBIg6y>42vO(B!LJ^8*IrZa${*3BM|Ls!Lh`wlO4>Oxkc9?7DR4s*Pq ztdSCNy^NM1>l&F?JhGuV?z=R`G(mv`E!KByG0-3^&bNcu2zrYl(ARbGxHp_BLcVkC z25&0oG403^uw9pet9xAl+0u}TMfD&Gn8w_q|4ujbVxI5TK zYatzxLWDlEI@F$S-pUF2a+xg7w$-hU)(t=PYQO77^3jkxub2BV@pl=8ZJLop+|!hi zVT+*>FTC%GBlOrhsoWZPlSKQK%Bxzu)1RrwBFlP<#fzG}N}p-?8ugkD=xe5y^tWYt zb;QhWnM;$P8;lJ(NssVzJ=dNVrSB0%w$@_1+t>l@ElI=XMXl=~B@a?FF58A4vE%Em zo6q{UGa~#Kl{Oss_4|?|!AkCHbi3|I-({j<^?E+ta_{`}ad$~U*Hf|AlX!3Is_#Zm zoE))V5@TsTFa$3r(KC;$sZhX~v9iP7`|U?4wG(xpubf>oN&_Xs(u#`2wmFv`vht?F=5s zT~GDs-V1Xy$IA##e2ix?O!1T}Q%VvrzRqXMy4f&Bx*b$jZFWQCH zOy`4{_#5_ExQo7Dq?F`!6Ya~x)6HjQ!h_Gd;37&KoX4Bw06l*WeP#;Qe6S3=M!tu85#iK zhVeJx5d8xjXBQ89E9WcNZ0c%gAcg3gwzYJdW7yb%sUx7yF`E>;XclHQ=~RR=-x+76 zk@eC3sigX7a68AdFp45hq+rY8+3v<0*M!KVxz#w^j>OFQRW3w$uj-O&vWRzMs-H|p zw=Rowds3dr7f6uc2uVZ*QK2|RK4n0lsEDDSfge74!Xs@`=R8}UdF5BtAj;4NLe*04 zo@iD)M%8vFTHJOv^&9m-XEUPSF-`sQVTEq-Sva6j_`dNLc*%5$H%a@(iy%=vsQ^*# z#4oFe&loo5*~6^!Ao2#dGUma8%D@MCIn0G<9L~}_&aJy7hoLiK0>DlWrd~`hkeaPI z|2Ui&W9)!Rji?8#Yb!W9ah~5WmKVXni6M_{{cs3gDX$6bTVqZX(d1D+a=6`rH6Qwo z@gz5UkyiDFIsrj@dQy^IX)y+;c`5mjp7WP6 z?EO}n);;qb@2;hbJ1^ZUF&-g4`jQ;=Qe_a#y&BnWSIReFf0|a~lpgzxxj6C3C(tHk z`9^KcDGz@i{o*VYtBTIguu8;R|3Xf+H7tLhaMk5a#7@6%C`ju~F@1RuEbMa}?b$3mlQKgr;a;dfm}k1963S67%yTY^MI)$vDS!p13RPT!N}|tdZRQ#fk7zBvmpB$dZ~ZYp0l-; 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is_deeply($message_hash->{'success'}, 1); my $added_seedlot2 = $message_hash->{'added_seedlot'}; -$file = $f->config->{basepath}."/t/data/stock/seedlot_inventory_android_app"; +#test seedlot_inventory csv upload with weight info +$file = $f->config->{basepath}."/t/data/stock/seedlot_inventory_android_app.csv"; $ua = LWP::UserAgent->new; $response = $ua->post( 'http://localhost:3010/ajax/breeders/seedlot-inventory-upload', Content_Type => 'form-data', Content => [ - seedlot_uploaded_inventory_file => [ $file, 'seedlot_inventory_upload', Content_Type => 'application/vnd.ms-excel', ], + seedlot_uploaded_inventory_file => [ $file, 'seedlot_inventory_android_app.csv'], "sgn_session_id"=>$sgn_session_id ] ); @@ -120,9 +121,53 @@ $response = $ua->post( ok($response->is_success); $message = $response->decoded_content; $message_hash = JSON::XS->new()->decode($message); -print STDERR Dumper $message_hash; +#print STDERR Dumper $message_hash; is_deeply($message_hash, {'success' => 1}); +my $seedlot4_stock_id = $schema->resultset('Stock::Stock')->find({ name => 'test_accession4_001' })->stock_id(); +my $seedlot4 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot4_stock_id); +my $seedlot4_weight = $seedlot4->current_weight; +is($seedlot4_weight, 10); + +my $seedlot3_stock_id = $schema->resultset('Stock::Stock')->find({ name => 'test_accession3_001' })->stock_id(); +my $seedlot3 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot3_stock_id); +my $seedlot3_weight = $seedlot3->current_weight; +is($seedlot3_weight, 12); + +my $seedlot2_stock_id = $schema->resultset('Stock::Stock')->find({ name => 'test_accession2_001' })->stock_id(); +my $seedlot2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot2_stock_id); +my $seedlot2_weight = $seedlot2->current_weight; +is($seedlot2_weight, 0); + +#test seedlot_inventory xlsx upload with amount info +$file = $f->config->{basepath}."/t/data/stock/seedlot_inventory_amount.xlsx"; +$ua = LWP::UserAgent->new; +$response = $ua->post( + 'http://localhost:3010/ajax/breeders/seedlot-inventory-upload', + Content_Type => 'form-data', + Content => [ + seedlot_uploaded_inventory_file => [ $file, 'seedlot_inventory_amount.xlsx', Content_Type => 'application/vnd.ms-excel'], + "sgn_session_id"=>$sgn_session_id + ] + ); + +ok($response->is_success); +$message = $response->decoded_content; +$message_hash = JSON::XS->new()->decode($message); +is_deeply($message_hash, {'success' => 1}); + +my $seedlot4_2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot4_stock_id); +my $seedlot4_count = $seedlot4_2->current_count; +is($seedlot4_count, 100); + +my $seedlot3_2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot3_stock_id); +my $seedlot3_count = $seedlot3_2->current_count; +is($seedlot3_count, 110); + +my $seedlot2_2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot2_stock_id); +my $seedlot2_count = $seedlot2_2->current_count; +is($seedlot2_count, 120); + #test seedlot list details my $seedlot_list_id = CXGN::List::create_list($f->dbh(), 'test_seedlot_list', 'test_desc', 41); my $seedlot_list = CXGN::List->new( { dbh => $f->dbh(), list_id => $seedlot_list_id } ); From a2fcbdd23333292dba7e671b62f175f3588a3a1f Mon Sep 17 00:00:00 2001 From: titima15 Date: Thu, 12 Feb 2026 17:00:59 -0500 Subject: [PATCH 8/9] modify test --- t/data/stock/seedlot_inventory_amount.xlsx | Bin 5090 -> 5368 bytes t/unit_mech/AJAX/Stocks/UploadSeedlots.t | 4 ---- 2 files changed, 4 deletions(-) diff --git a/t/data/stock/seedlot_inventory_amount.xlsx b/t/data/stock/seedlot_inventory_amount.xlsx index 500646fec7b99f68522ad2eb0de44be84ef9dd7d..6d61dc9f05243629ee225e17ceda62897ff1808a 100644 GIT binary patch delta 4276 zcmZu!2QXai_uf@jx2%m2b*)}Ph#Evm)K$XjA)-WdmPB{4h!TVqJw*?ZMYL$qMf4ic zR*8s+E(sCkN9I4@C*S88oS>aQrVV8Vq%-0#vt z@(nxQLvpPr<~=o|y@+DgeeCeYjG3rwm)rDUmQ8`AyE z30clx*;-7qje1*eH_PkSUJRe?Se>$!OS?3{WkQ;2uH1XkdZKS-W;?G>am0UPD8Sy< z7$HS9TjNJ6S))1=lA}?i)0c><*l`7HL(W$dHJk6>phF#IP<680VC`R0&6f7vd2K(tQqA3~S*%S-)PIOx}u1-3kQm8g$2-z0W6gsvIs9 zo$%>Olv^+mFP$TwmuK1)0F>_Lp#)X?KWuT&*#Yk?Mi2x?q*bNL#hTh7gHC|DZ{9pE zDyQrC+(b3je=&XS$rp!g%AgqLSIgT=!I*J}8`jsUvf}T2BKVNmnB4BYGcRw$zP*~w zhVJDBD+ooDFUQEhb)T??u2eBfE;fDbS}VD#@ENjV6)9pQw?S3B>Kz7`qZAU?eAuU= z-#mRjQFZn9i_UnlASPWxDDzkIn?f z89$?>QSW1I9RoXv+@XxXr48$Ay}=F7)JE*2;vhqEtTe5g_r>?bF6cqNx@HW|CFzLk z0ZApSD`CN!>a#i7?u+2=wFu*Yb?)l>$${M~M{E*JChaTdPmvMpD{*dZ7YqWq5uZZi z3^FW<5rC!Mlo&i{wzTX(F)3N!S_{i$SlEcV3#V|L#A;@>w{j$|skD{O-peYWh|pPK zH_lU>*j;@3>65cXRp!kS67>W$OTi+wx;jD)eMivYb=Le;$H6CNwN6+%1D^ZIeB_0| z#9)nwt}=~9{8i-ey!83*$$dk*w33{#G^CLs1#pWppR}BAMO>_^fLl7A+gFUD&5@HF zC!@1y&>JDiZ>a6qq6S6G2KIonI+^@xg&t!cm!b`HWN3%Emq~{6^f9>%w$Qw2KedE# ztj6*%5B=!7)C|9fF!D|os4nXxqiZZ_PYSEBzC~;#ZH?JAaY78A8bn7(0yuS?Y(&N| zNLuj9er!RcxwdJb=*ZF`PyJ|KG%p{q%2e~4U9B%=6OmMFxD*lrV9=^|qj{70^Fim@ zbiIwlZ@OzH9Y1w(t{}2jzl}PpA}S5bojdrfs4?wH@Uy98dhhpU0;EBSzONqVr@KO} zs0t~}_;R!ye^L*-fqUF?>%E-JmN>88dMIo;!O;yXC3^bwa?yFv&+B&L?qref1;Z#s z;nA!g&$3bX+=)FOD+mk*y1urN)hA1DDfYclwo_jB#4((Z&^`M9pp6A049vPO$j}8hHF0&f zDbB!P&y}RhR+MWki!6$V8y~OtanqKsd^DR19d0`6ybn_eTQ4@O3gX=I-R|p^KH8Ez zI7qtTkPyM0)pxUL+=s1~i=Cl5vv&5GF$W(WdCuliPS$*SK>P5a{IQ6<$Cj|+!^gxR zRR1)(=wNckE_s3aJ-|M237Z}sOD(_@^MubU^oEOK_lxu2f16lEl6#4?R{2sv^kA@g zo`e``343Ld0uAMTah}?eL8}Gn`3@qs=c9tp)MB)+7=HTIMr)?*0oK@%Z=J} z6TJg4^;o4ev~l~B9}~lK{hAqineyd`Rrpm#j*I$Q8bY3Nm z-XL$YHp=0TOE@T-`%Xm%7J4bWB@O8m#B$cd#T(k9ixKB0-NZT)TRnH`?`89oOt4mn z6iO;RWI*fZ8v-F7H_<;8?Bu=D3vfi-1NWjx3(%=w0aQaa-;(51|bIa%jPGo7q&Gh=)ac~B!= z!qvqW0JUr#+I}!|a?H&nQ6VHzWk-J#i|nN=3tbC)Y5U{@Mu_6up=j(>`$jUE(KnC% z@}7Nx7X&u(vr$8qP+ae+)_^T zqd(r9zL;vrSNu`tB$5hguGrZo)X>~{!^^;)UQ8YP2;+52Xj2tks%5H_I`*Qvawf90 z{0l}o&HRg+p{&5oh38n^)T4Fp`5F;U`4x#!s_pJ{6>qQ#O>8Fxk&|KKi!1YHKelP2 z*+QE~yTXFq<(U(-UU^(-b#)qD;b$5L2Af4p2FtZ2iiWuOLc+bqm;$OWf|xgDUc!LX z;<^480{Y{0WNJ5zq+Mi7O3~v(bk4UI+7Fta8uWh97ZJXo{MG12@@I;fi`lIS11P%%YG0Vc}CT$H0ql$elogm;>^mAw*vY&rS-)`(|t4jmr)m#Bm^2 zKKn|=;$<97x=h{?R8+KA;R zu@OJH`t<~-E;PO@GJvOw^IR=#@uwF>X^^`X=|tyz;g zeB}hKPQ`$zN7OnrKOIQ^=?X7CQ2Gr%W$Aq0$L9q0P72fXM=qYx1pGAOfF(*oEhmys z6BTkd@a2p>dK~Xag$3Me%0s)c?z_`o{_7?c6UxRd><`aXWpKed_(2`tR9;|WKD_kv zO(6P~CTMCTl$L`uz1-t2ju$AUX-G52dJ?(J#U(gV%}o$>^@$=G21UMBD|+F?Gz%7qY6Z8q5 zmwn;UxXNu?tYF_!VzHO&P6CIjZ+P-Zdvoj60`bYiS5)}Ec4%OgO(vSHDgjZwx*ViS zeRX|;-W;C8kwo!+tI=TLgUtb;x9LyejgK=w+ns2!ssGgdEKn;(X$8PQCjRUm2*hx5 zTXycY`WSZ)FHzfjUf%Am7kyn_p7fVfwu-?c=4T4YC#KM3iNlq#GFQ;Mj|kOZFZV8; 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z`R_g46!D@Zz1eqs2}A|5RQ)S zsorc&)AyFc773VzZI7&?5v%EZxm3LQmZcrI@u76CNT_A1F#DnmQeJplg9frkqh?hmP^8y z!Y!~LLdnExOdYZn$ewNzl-DVEqy;IwjCKtO6faXfwtk1hX8|iga3P7ziU=h7Xz31FU&u-=pR=^ z^B3mk`CPuPlAd0Et`43OzV}`Kz2g7m3j|{QYbY3Xg;DVL7W97{`j4FV@t;$O?JrC_ zDx6XHH|Ec`4fzW*jp}FQ{f+sPis%0AkHUeXg+PC4r4)pN;4MlQ!VUd(u0KP?_y-&W W+6JQrAe^)mAPSJ``L3S+p6)+Il@fUX diff --git a/t/unit_mech/AJAX/Stocks/UploadSeedlots.t b/t/unit_mech/AJAX/Stocks/UploadSeedlots.t index a31274ced1..91a4c2be87 100644 --- a/t/unit_mech/AJAX/Stocks/UploadSeedlots.t +++ b/t/unit_mech/AJAX/Stocks/UploadSeedlots.t @@ -156,10 +156,6 @@ $message = $response->decoded_content; $message_hash = JSON::XS->new()->decode($message); is_deeply($message_hash, {'success' => 1}); -my $seedlot4_2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot4_stock_id); -my $seedlot4_count = $seedlot4_2->current_count; -is($seedlot4_count, 100); - my $seedlot3_2 = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot3_stock_id); my $seedlot3_count = $seedlot3_2->current_count; is($seedlot3_count, 110); From 0db2646d93fc5ac526f13a31c8c1be140a89473b Mon Sep 17 00:00:00 2001 From: titima15 Date: Fri, 20 Feb 2026 12:29:24 -0500 Subject: [PATCH 9/9] fix typo --- .../Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm index bd6819f092..6f9434eda7 100644 --- a/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm +++ b/lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm @@ -55,7 +55,7 @@ sub _validate_with_plugin { for my $row ( @$parsed_data ) { my $row_num = $row->{_row}; - my $seedlot_name = $row->{'seedlot_id'}; + my $seedlot_name = $row->{'seed_id'}; my $amount = $row->{'amount'}; my $weight = $row->{'weight_gram'}; @@ -64,11 +64,10 @@ sub _validate_with_plugin { } } - my $seen_seedlot_names = $parsed_values->{'seedlot_id'}; + my $seen_seedlot_names = $parsed_values->{'seed_id'}; my $seedlot_validator = CXGN::List::Validate->new(); my @seedlots_missing = @{$seedlot_validator->validate($schema,'seedlots',$seen_seedlot_names)->{'missing'}}; - if (scalar(@seedlots_missing) > 0) { push @error_messages, "The following seedlots are not in the database as uniquenames: ".join(',',@seedlots_missing); }