Allow seedlot inventory upload to use count (in addition to weight) and change to generic plugin

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+# DEPRECATED: This plugin has been replaced by the SeedlotInventoryGeneric plugin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();

lib/CXGN/Stock/Seedlot/ParseUpload/Plugin/SeedlotInventoryGeneric.pm

@@ -0,0 +1,139 @@
+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'],
+            'amount' => ['count'],
+
+        },
+    );
+
+    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->{'seed_id'};
+        my $amount = $row->{'amount'};
+        my $weight = $row->{'weight_gram'};
+
+        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.";
+        }
+    }
+
+    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);
+    }
+
+    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;
+        my $amount;
+        $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 = $row->{'weight_gram'};
+        $amount = $row->{'amount'};
+        $seen_seedlot_names{$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,
+            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){
+        $parsed_result{$r->uniquename}{seedlot_id} = $r->stock_id;
+    }
+
+    $self->_set_parsed_data(\%parsed_result);
+
+    return 1;
+
+}
+
+
+1;

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;
 
@@ -907,46 +907,54 @@ sub upload_seedlots_inventory_POST : Args(0) {
         $c->stash->{rest} = {error_string => $return_error, missing_seedlots => $parse_errors->{'missing_seedlots'} };
         $c->detach();
     }
-
     eval {
         while (my ($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();
+	        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
+            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 {
+                    $factor = -1;
+                    $weight_difference = $weight_difference * -1; #Store positive values only
+                }
+            }
+
+            if (defined $inventory_amount) {
+                $amount_difference = $inventory_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 = $val->{seedlot_name};
-
-	    if ($val->{source_id}) {
-		$from_stock_id = $val->{source_id};
-		$from_stock_name = $val->{source};
-	    }
-
+            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);
+            if (defined $inventory_weight) {
+                $transaction->weight_gram($weight_difference);
+            } elsif (defined $inventory_amount) {
+                $transaction->amount($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();
 

mason/breeders_toolbox/upload_seedlots_inventory_dialogs.mas

@@ -154,10 +154,6 @@
             </div>
             <div class="modal-body">
                 <div class="container-fluid">
-                    <b>Seedlots may be uploaded in a CSV file (.csv)</b>
-                    <br />
-                    (Excel .xls and .xlsx format not supported)
-                    <br /><br />
                     <b>Header:</b>
                     <br>
                     The first row (header) should contain the following:
@@ -175,17 +171,23 @@
                             </tr>
                         </tbody>
                     </table>
-
+                    <b>Note: If you would like to upload number of materials in seedlot instead of weight, you can replace the header 'weight_gram' with 'amount'</b>
+                    <br/>
+                    <br/>
                     <b>Required fields:</b>
                     <ul>
                     <li>box_id (the name of the box that the seedlot is in. also called box_name.)</li>
                     <li>seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)</li>
                     <li>inventory_date (a timestamp for when the seedlot was inventoried)</li>
                     <li>inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)</li>
-                    <li>weight_gram (the weight in grams of the seedlot)</li>
+                    <li>weight_gram (the weight in grams of the seedlot)
+                    <br/><b>OR</b><br/>
+                    amount (number of materials in seedlot.)</li>
+
                     </ul>
 
                 </div>
+                <& /help/file_upload_type.mas, type => "Seedlot Inventory", optional_column => 0 &>
             </div>
             <div class="modal-footer">
                 <button id="close_seedlot_info_upload_inventory_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>

t/unit_mech/AJAX/Stocks/UploadSeedlots.t

@@ -105,13 +105,14 @@ my $message_hash = JSON::XS->new()->decode($message);
 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 +121,49 @@ $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 $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 } );