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perltidy
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@sajp
sajp committed Jul 27, 2012
1 parent 56b22ef commit 38305b1
Showing 1 changed file with 55 additions and 44 deletions.
99 changes: 55 additions & 44 deletions lib/LIMS2/Model/Plugin/Plate.pm
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Expand Up @@ -14,17 +14,18 @@ requires qw( schema check_params throw retrieve log trace );
sub list_plate_types {
my $self = shift;

return [ $self->schema->resultset('PlateType')->search( {}, { order_by => { -asc => 'id' } } ) ];
return [
$self->schema->resultset('PlateType')->search( {}, { order_by => { -asc => 'id' } } ) ];
}

sub pspec_list_plates {
return {
species => { validate => 'existing_species' },
plate_name => { validate => 'non_empty_string', optional => 1 },
plate_name => { validate => 'non_empty_string', optional => 1 },
plate_type => { validate => 'existing_plate_type', optional => 1 },
page => { validate => 'integer', optional => 1, default => 1 },
pagesize => { validate => 'integer', optional => 1, default => 15 }
}
page => { validate => 'integer', optional => 1, default => 1 },
pagesize => { validate => 'integer', optional => 1, default => 15 }
};
}

sub list_plates {
Expand All @@ -35,7 +36,8 @@ sub list_plates {
my %search = ( 'me.species_id' => $validated_params->{species} );

if ( $validated_params->{plate_name} ) {
$search{'me.name'} = { -like => '%' . sanitize_like_expr( $validated_params->{plate_name} ) . '%' };
$search{'me.name'}
= { -like => '%' . sanitize_like_expr( $validated_params->{plate_name} ) . '%' };
}

if ( $validated_params->{plate_type} ) {
Expand All @@ -44,8 +46,7 @@ sub list_plates {

my $resultset = $self->schema->resultset('Plate')->search(
\%search,
{
prefetch => [ 'created_by' ],
{ prefetch => ['created_by'],
order_by => { -desc => 'created_at' },
page => $validated_params->{page},
rows => $validated_params->{pagesize}
Expand Down Expand Up @@ -90,8 +91,13 @@ sub create_plate {
my $validated_params = $self->check_params( $params, $self->pspec_create_plate );

my $plate = $self->schema->resultset('Plate')->create(
{ slice_def( $validated_params, qw( name species_id type_id description created_by_id created_at ) ) }
{ slice_def(
$validated_params,
qw( name species_id type_id description created_by_id created_at )
)
}
);

# refresh object data from database, sets created_by value
# if it was set by database
$plate->discard_changes;
Expand All @@ -111,20 +117,22 @@ sub create_plate {

sub pspec_retrieve_plate {
return {
name => { validate => 'plate_name', optional => 1, rename => 'me.name' },
id => { validate => 'integer', optional => 1, rename => 'me.id' },
type => { validate => 'existing_plate_type', optional => 1, rename => 'me.type_id' },
species => { validate => 'existing_species', rename => 'me.species_id', optional => 1 },
name => { validate => 'plate_name', optional => 1, rename => 'me.name' },
id => { validate => 'integer', optional => 1, rename => 'me.id' },
type => { validate => 'existing_plate_type', optional => 1, rename => 'me.type_id' },
species => { validate => 'existing_species', rename => 'me.species_id', optional => 1 },
REQUIRE_SOME => { name_or_id => [ 1, qw( name id ) ] }
};
}

sub retrieve_plate {
my ( $self, $params ) = @_;

my $validated_params = $self->check_params( $params, $self->pspec_retrieve_plate, ignore_unknown => 1 );
my $validated_params
= $self->check_params( $params, $self->pspec_retrieve_plate, ignore_unknown => 1 );

return $self->retrieve( Plate => { slice_def $validated_params, qw( me.name me.id me.type_id me.species_id ) } );
return $self->retrieve(
Plate => { slice_def $validated_params, qw( me.name me.id me.type_id me.species_id ) } );
}

sub delete_plate {
Expand All @@ -137,7 +145,7 @@ sub delete_plate {
$self->delete_well( { id => $well->id } );
}

$plate->search_related_rs( 'plate_comments' )->delete;
$plate->search_related_rs('plate_comments')->delete;
$plate->delete;
return;
}
Expand All @@ -151,14 +159,14 @@ sub pspec_set_plate_assay_complete {
sub set_plate_assay_complete {
my ( $self, $params ) = @_;

my $validated_params = $self->check_params( $params, $self->pspec_set_plate_assay_complete, ignore_unknown => 1 );
my $validated_params = $self->check_params( $params, $self->pspec_set_plate_assay_complete,
ignore_unknown => 1 );

my $plate = $self->retrieve_plate( $params );
my $plate = $self->retrieve_plate($params);

for my $well ( $plate->wells ) {
$self->set_well_assay_complete(
{
id => $well->id,
{ id => $well->id,
completed_at => $validated_params->{completed_at}
}
);
Expand All @@ -179,9 +187,10 @@ sub pspec_create_plate_well {
sub create_plate_well {
my ( $self, $params, $plate ) = @_;

my $validated_params = $self->check_params( $params, $self->pspec_create_plate_well, ignore_unknown => 1 );
my $validated_params
= $self->check_params( $params, $self->pspec_create_plate_well, ignore_unknown => 1 );

my $parent_well_ids = $self->find_parent_well_ids( $params );
my $parent_well_ids = $self->find_parent_well_ids($params);

my %well_params = (
plate_name => $plate->name,
Expand All @@ -191,49 +200,52 @@ sub create_plate_well {
);

# the remaining params are specific to the process
delete @{$params} {qw( well_name process_type )};
delete @{$params}{qw( well_name process_type )};

$well_params{process_data} = $params;
$well_params{process_data}{type} = $validated_params->{process_type};
$well_params{process_data}{input_wells} = [ map{ { id => $_ } } @{ $parent_well_ids } ];
$well_params{process_data} = $params;
$well_params{process_data}{type} = $validated_params->{process_type};
$well_params{process_data}{input_wells} = [ map { { id => $_ } } @{$parent_well_ids} ];

$self->create_well( \%well_params, $plate );
}

sub pspec_find_parent_well_ids {
return {
parent_plate => { validate => 'plate_name', optional => 1 },
parent_well => { validate => 'well_name', optional => 1 },
allele_plate => { validate => 'plate_name', optional => 1 },
allele_well => { validate => 'well_name', optional => 1 },
vector_plate => { validate => 'plate_name', optional => 1 },
vector_well => { validate => 'well_name', optional => 1 },
DEPENDENCY_GROUPS => { parent => [qw( parent_plate parent_well )] },
DEPENDENCY_GROUPS => { vector => [qw( vector_plate vector_well )] },
DEPENDENCY_GROUPS => { allele => [qw( allele_plate allele_well )] },
parent_plate => { validate => 'plate_name', optional => 1 },
parent_well => { validate => 'well_name', optional => 1 },
allele_plate => { validate => 'plate_name', optional => 1 },
allele_well => { validate => 'well_name', optional => 1 },
vector_plate => { validate => 'plate_name', optional => 1 },
vector_well => { validate => 'well_name', optional => 1 },
DEPENDENCY_GROUPS => { parent => [qw( parent_plate parent_well )] },
DEPENDENCY_GROUPS => { vector => [qw( vector_plate vector_well )] },
DEPENDENCY_GROUPS => { allele => [qw( allele_plate allele_well )] },
};
}

sub find_parent_well_ids {
my ( $self, $params ) = @_;

my $validated_params = $self->check_params( $params, $self->pspec_find_parent_well_ids, ignore_unknown => 1 );
my $validated_params
= $self->check_params( $params, $self->pspec_find_parent_well_ids, ignore_unknown => 1 );

my @parent_well_ids;

if ( $params->{process_type} eq 'second_electroporation' ) {
push @parent_well_ids,
$self->get_well_id( $validated_params->{allele_plate}, $validated_params->{allele_well} );
$self->get_well_id( $validated_params->{allele_plate},
$validated_params->{allele_well} );

push @parent_well_ids,
$self->get_well_id( $validated_params->{vector_plate}, $validated_params->{vector_well} );
$self->get_well_id( $validated_params->{vector_plate},
$validated_params->{vector_well} );

delete @{$params}
{qw( allele_plate vector_plate allele_well vector_well )};
delete @{$params}{qw( allele_plate vector_plate allele_well vector_well )};
}
else {
push @parent_well_ids,
$self->get_well_id( $validated_params->{parent_plate}, $validated_params->{parent_well} );
$self->get_well_id( $validated_params->{parent_plate},
$validated_params->{parent_well} );

delete @{$params}{qw( parent_plate parent_well )};
}
Expand All @@ -245,9 +257,8 @@ sub get_well_id {
my ( $self, $plate_name, $well_name ) = @_;

my $well = $self->retrieve_well(
{
plate_name => $plate_name,
well_name => substr( $well_name, -3),
{ plate_name => $plate_name,
well_name => substr( $well_name, -3 ),
}
);

Expand Down

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