fixed merge conflict

db/00181/AddDiscardedMetadataCvterm.pm

@@ -0,0 +1,74 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+AddDiscardedMetadataCvterm
+
+=head1 SYNOPSIS
+
+mx-run AddDiscardedMetadataCvterm [options] -H hostname -D dbname -u username [-F]
+
+this is a subclass of L<CXGN::Metadata::Dbpatch>
+see the perldoc of parent class for more details.
+
+=head1 DESCRIPTION
+This patch adds discarded_metadata stock_property cvterm
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Titima Tantikanjana <[email protected]>
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2010 Boyce Thompson Institute for Plant Research
+
+This program is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+
+package AddDiscardedMetadataCvterm;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch adds the 'discarded_metadata' stock_property cvterm
+
+has '+prereq' => (
+	default => sub {
+        [],
+    },
+
+);
+
+sub patch {
+    my $self=shift;
+
+    print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
+
+    print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
+
+    print STDOUT "\nExecuting the SQL commands.\n";
+    my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
+
+    print STDERR "INSERTING CV TERMS...\n";
+
+    $schema->resultset("Cv::Cvterm")->create_with({
+        name => 'discarded_metadata',
+        cv => 'stock_property'
+    });
+
+    print "You're done!\n";
+}
+
+
+####
+1; #
+####

lib/CXGN/List.pm

@@ -772,7 +772,7 @@ sub seedlot_list_details {
             $content_type = 'cross';
         }
 
-        push @seedlot_details, [$id, $seedlot_obj->uniquename(), $content_id, $content_name, $content_type, $seedlot_obj->box_name(), $seedlot_obj->get_current_count_property(), $seedlot_obj->get_current_weight_property(), $seedlot_obj->quality()];
+        push @seedlot_details, [$id, $seedlot_obj->uniquename(), $content_id, $content_name, $content_type, $seedlot_obj->description(), $seedlot_obj->box_name(), $seedlot_obj->get_current_count_property(), $seedlot_obj->get_current_weight_property(), $seedlot_obj->quality()];
 
     }
 

lib/CXGN/Stock/Seedlot/Discard.pm

@@ -0,0 +1,75 @@
+
+package CXGN::Stock::Seedlot::Discard;
+
+=head1 NAME
+
+CXGN::Stock::Seedlot::Discard
+
+=head1 DESCRIPTION
+
+Store and manage discarded seedlot metadata
+
+=head1 USAGE
+
+
+=head1 AUTHOR
+
+Titima Tantikanjana <[email protected]>
+
+=cut
+
+
+use Moose;
+use Data::Dumper;
+
+
+extends 'CXGN::JSONProp';
+
+has 'person_id' => (isa => 'Int', is => 'rw');
+has 'discard_date' => (isa => 'Str', is => 'rw');
+has 'reason' => (isa => 'Str', is => 'rw');
+
+
+sub BUILD {
+    my $self = shift;
+    my $args = shift;
+
+    $self->prop_table('stockprop');
+    $self->prop_namespace('Stock::Stockprop');
+    $self->prop_primary_key('stockprop_id');
+    $self->prop_type('discarded_metadata');
+    $self->cv_name('stock_property');
+    $self->allowed_fields([ qw | person_id discard_date reason | ]);
+    $self->parent_table('stock');
+    $self->parent_primary_key('stock_id');
+
+    $self->load();
+}
+
+
+sub get_discard_details {
+    my $self = shift;
+    my $args = shift;
+    my $schema = $self->bcs_schema();
+    my $seedlot_id = $self->parent_id();
+    my $type = $self->prop_type();
+    my $type_id = $self->_prop_type_id();
+    my $key_ref = $self->allowed_fields();
+    my @fields = @$key_ref;
+    my @discard_details;
+    my $discard_details_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $seedlot_id, type_id => $type_id});
+    if ($discard_details_rs) {
+        my $details_json = $discard_details_rs->value();
+        my $detail_hash = JSON::Any->jsonToObj($details_json);
+        foreach my $field (@fields){
+            push @discard_details, $detail_hash->{$field};
+        }
+        print STDERR "DISCARDED DETAILS =".Dumper(\@discard_details)."\n";
+    }
+
+    return \@discard_details;
+}
+
+
+
+1;

lib/SGN/Controller/AJAX/HTMLSelect.pm

@@ -480,7 +480,7 @@ sub get_label_data_source_types_select : Path('/ajax/html/select/label_data_sour
     my @types = (
         ["any", "Any Data Type..."],
         ["field_trials", "Field Trials"],
-        ["genotyping_plates", "Genotyping Plates"], 
+        ["genotyping_plates", "Genotyping Plates"],
         ["crossing_experiments", "Crossing Experiments"],
         ["lists", "Lists"],
         ["public_lists", "Public Lists"]
@@ -720,6 +720,7 @@ sub get_seedlots_select : Path('/ajax/html/select/seedlots') Args(0) {
 #    my $search_location = $c->req->param('seedlot_location') ? $c->req->param('seedlot_location') : '';
 #    my $search_amount = $c->req->param('seedlot_amount') ? $c->req->param('seedlot_amount') : '';
 #    my $search_weight = $c->req->param('seedlot_weight') ? $c->req->param('seedlot_weight') : '';
+    my $exclude_discarded = $c->req->param('exclude_discarded') ? $c->req->param('exclude_discarded') : '';
     my ($list, $records_total) = CXGN::Stock::Seedlot->list_seedlots(
         $c->dbic_schema("Bio::Chado::Schema", "sgn_chado"),
         $c->dbic_schema("CXGN::People::Schema"),
@@ -757,7 +758,13 @@ sub get_seedlots_select : Path('/ajax/html/select/seedlots') Args(0) {
     my $data_related = $c->req->param("data-related") || "";
     my @stocks;
     foreach my $r (@seedlots) {
-        push @stocks, [ $r->{seedlot_stock_id}, $r->{seedlot_stock_uniquename} ];
+        if ($exclude_discarded == 1) {
+            if ($r->{count} ne 'DISCARDED') {
+                push @stocks, [ $r->{seedlot_stock_id}, $r->{seedlot_stock_uniquename} ];
+            }
+        } else {
+            push @stocks, [ $r->{seedlot_stock_id}, $r->{seedlot_stock_uniquename} ];
+        }
     }
     @stocks = sort { $a->[1] cmp $b->[1] } @stocks;
 

lib/SGN/Controller/AJAX/List.pm

@@ -1313,10 +1313,11 @@ sub get_list_details :Path('/ajax/list/details') :Args(1) {
                 content_id => $seedlot->[2],
                 content_name => $seedlot->[3],
                 content_type => $seedlot->[4],
-                box_name => $seedlot->[5],
-                current_count => $seedlot->[6],
-                current_weight => $seedlot->[7],
-                quality => $seedlot->[8],
+                description => $seedlot->[5],
+                box_name => $seedlot->[6],
+                current_count => $seedlot->[7],
+                current_weight => $seedlot->[8],
+                quality => $seedlot->[9],
             }
         }
     }
@@ -1345,9 +1346,9 @@ sub download_list_details : Path('/list/download_details') {
         my @details = @$result;
         foreach my $seedlot_ref (@details) {
             my @seedlot = @$seedlot_ref;
-            push @list_details, "$seedlot[1]\t$seedlot[3]\t$seedlot[4]\t$seedlot[5]\t$seedlot[6]\t$seedlot[7]\t$seedlot[8]\n";
+            push @list_details, "$seedlot[1]\t$seedlot[3]\t$seedlot[4]\t$seedlot[5]\t$seedlot[6]\t$seedlot[7]\t$seedlot[8]\t$seedlot[9]\n";
         }
-        $header = "Seedlot_Name\tContent_Name\tContent_type\tBox_Name\tCurrent_Count\tCurrent_Weight\tQuality";
+        $header = "Seedlot_Name\tContent_Name\tContent_type\tDescription\tBox_Name\tCurrent_Count\tCurrent_Weight\tQuality";
     }
 
     my $dl_token = $c->req->param("list_download_token") || "no_token";

lib/SGN/Controller/AJAX/Seedlot.pm

@@ -17,6 +17,9 @@ use CXGN::Login;
 use JSON;
 use CXGN::BreederSearch;
 use CXGN::Onto;
+use CXGN::List;
+use CXGN::List::Validate;
+use CXGN::Stock::Seedlot::Discard;
 
 __PACKAGE__->config(
     default   => 'application/json',
@@ -1616,6 +1619,127 @@ sub seedlot_maintenance_event_upload_POST : Args(0) {
     $c->stash->{rest} = { success => 1 };
 }
 
+
+sub discard_seedlots : Path('/ajax/breeders/seedlot/discard') :Args(0) {
+    my $self = shift;
+    my $c = shift;
+    my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
+    my $dbh = $c->dbc->dbh();
+    my $seedlot_list_id = $c->req->param("seedlot_list_id");
+    my $seedlot_name = $c->req->param("seedlot_name");
+    my $discard_reason = $c->req->param("discard_reason");
+    my @seedlots_to_discard;
+
+    my $time = DateTime->now();
+    my $discard_date = $time->ymd();
+
+    if (!$c->user()){
+        $c->stash->{rest} = { error_string => "You must be logged in to discard seedlot" };
+        return;
+    }
+    if (!$c->user()->check_roles("curator")) {
+        $c->stash->{rest} = { error_string => "You do not have the correct role to discard seedlot. Please contact us." };
+        return;
+    }
+
+    my $user_id = $c->user()->get_object()->get_sp_person_id();
+
+    if (defined $seedlot_list_id) {
+        my $list = CXGN::List->new( { dbh=>$dbh, list_id=>$seedlot_list_id });
+        my $seedlots = $list->elements();
+        @seedlots_to_discard = @$seedlots;
+
+        my $seedlot_validator = CXGN::List::Validate->new();
+        my @seedlots_missing = @{$seedlot_validator->validate($schema,'seedlots',\@seedlots_to_discard)->{'missing'}};
+
+        if (scalar(@seedlots_missing) > 0){
+            $c->stash->{rest} = { error_string => "The following seedlots are not in the database : ".join(',',@seedlots_missing) };
+            return;
+        }
+    } elsif (defined $seedlot_name) {
+        @seedlots_to_discard = ($seedlot_name);
+    }
+
+    my $seedlot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "seedlot", 'stock_type')->cvterm_id();
+    my $current_count_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "current_count", 'stock_property')->cvterm_id();
+    my $current_weight_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "current_weight_gram", 'stock_property')->cvterm_id();
+
+    foreach my $seedlot_name (@seedlots_to_discard) {
+        my $seedlot_rs = $schema->resultset("Stock::Stock")->find( { uniquename => $seedlot_name, type_id => $seedlot_type_id });
+        my $seedlot_id = $seedlot_rs->stock_id();
+
+        my $current_count_rs = $seedlot_rs->stockprops({type_id=>$current_count_type_id});
+        if ($current_count_rs->count == 1){
+            $current_count_rs->first->update({value=>'DISCARDED'});
+        }
+
+        my $current_weight_rs = $seedlot_rs->stockprops({type_id=>$current_weight_type_id});
+        if ($current_weight_rs->count == 1){
+            $current_weight_rs->first->update({value=>"DISCARDED"});
+        }
+
+        my $seedlot_to_discard = CXGN::Stock::Seedlot::Discard->new({
+            bcs_schema => $schema,
+            parent_id => $seedlot_id,
+        });
+
+        $seedlot_to_discard->person_id($user_id);
+        $seedlot_to_discard->discard_date($discard_date);
+        $seedlot_to_discard->reason($discard_reason);
+
+        $seedlot_to_discard->store();
+
+        if (!$seedlot_to_discard->store()){
+            $c->stash->{rest} = {error_string => "Error discarding seedlot",};
+            return;
+        }
+    }
+
+    my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
+    my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'stockprop', 'concurrent', $c->config->{basepath});
+
+    $c->stash->{rest} = {success => "1",};
+
+}
+
+
+sub undo_discarded_seedlots : Path('/ajax/breeders/seedlot/undo_discard') :Args(0) {
+    my $self = shift;
+    my $c = shift;
+    my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
+    my $dbh = $c->dbc->dbh();
+    my $seedlot_id = $c->req->param("seedlot_id");
+
+    if (!$c->user()){
+        $c->stash->{rest} = { error_string => "You must be logged in to undo discading this seedlot" };
+        return;
+    }
+    if (!$c->user()->check_roles("curator")) {
+        $c->stash->{rest} = { error_string => "You do not have the correct role to undo discarding this seedlot. Please contact us." };
+        return;
+    }
+
+    my $user_id = $c->user()->get_object()->get_sp_person_id();
+
+    my $discarded_metadata_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'discarded_metadata', 'stock_property')->cvterm_id();
+    my $discarded_rs = $schema->resultset("Stock::Stockprop")->find({stock_id => $seedlot_id, type_id => $discarded_metadata_type_id});
+
+    if (defined $discarded_rs->stockprop_id) {
+        $discarded_rs->delete();
+    }
+
+    my $restored_seedlot = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id => $seedlot_id);
+    $restored_seedlot->set_current_count_property();
+    $restored_seedlot->set_current_weight_property();
+
+    my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
+    my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'stockprop', 'concurrent', $c->config->{basepath});
+
+    $c->stash->{rest} = { success => 1 };
+
+}
+
+
 1;
 
 no Moose;