package LIMS::Controller::Local::Worklist; # only ucfirst or need an entry in Dispatch

# provides methods for local worklists - requires entry in config/.local/worklists.yml

use base 'LIMS::Base';

use Moose;
with (
	'LIMS::Controller::Roles::PDF',
	'LIMS::Controller::Roles::Misc',
	'LIMS::Controller::Roles::Barcode',
	'LIMS::Controller::Roles::History',
	'LIMS::Controller::Roles::DataMap',
	'LIMS::Controller::Roles::DataFile',
);

has 'tt_name' => (is => 'rw', isa => 'Str');

use Data::Dumper;
use Array::Diff;
use IO::All;

__PACKAGE__->meta->make_immutable(inline_constructor => 0);

# ------------------------------------------------------------------------------
sub default : StartRunmode {
	my $self = shift; $self->_debug_path($self->get_current_runmode);

	# get function_name from query param, or return to start (in case user cleared menu):
	my $function_name = $self->query->param('function_name')
	|| return $self->redirect( $self->query->url . '/worklist' ); # warn $function_name;

	# check method exists or return error:
	unless ( UNIVERSAL::can($self, $function_name) ) {
		return $self->error( qq!no method  "$function_name" found at !
		. $self->get_current_runmode );
	}

	# process method - all tmpl data handled in method
	do{ $self->$function_name }; # don't need rtn value - returns 0 if no hits
    #    or return $self->error($function_name.'() did not return a true value');

	# use render_view to override default template name (unless supplied in rm):
	$self->tt_name || $self->tt_name('worklist/local/'.$function_name.'.tt');
	return $self->render_view($self->tt_name, {}); # tt_params set in methods
}

# ------------------------------------------------------------------------------
# collects outstanding data from flow_screen table, for fresh tissue samples only
# formats request number in '%02d_%05d' format
#
sub pre_screen : Runmode {
    my $self = shift; $self->_debug_path(); # not called directly

	# optional list of lab-tests
	my @tests = $self->query->param('test_name'); # warn Dumper \@tests;
	# optional lab-test status:
    my $status_option_id = $self->query->param('status_option_id'); # warn Dumper $status_option_id;

    # get Flow cytometry lab_section object (used by flow screen data & status opts)
	my $lab_section
        = $self->model('LabSection')->get_lab_section_by_name('Flow cytometry');

	{ # get data for flow screen panels:
        # need to supply list of lab_test id's to model:
        my $lab_test_names = @tests
			? \@tests
			: $self->get_yaml_file('pre_screen_panel'); # warn Dumper $lab_test_names;

		# hash map for tt:
		my %included_lab_tests = map +($_ => 1), @$lab_test_names;
		$self->tt_params( included_lab_tests => \%included_lab_tests );

        my $lab_tests = do {
            my %args = (
                section_name => 'Flow cytometry',
                test_name    => $lab_test_names, # arrayref
            );
            $self->model('LabTest')->get_section_lab_tests(\%args);
        }; # warn Dumper $lab_tests;
		my @lab_test_ids = map { $_->id } @$lab_tests;
        return 1 unless @lab_test_ids; # or will get error in downstream model

		# get outstanding flow screen investigations:
        my $args = {
            status_option_id => $status_option_id,
            lab_test_id      => \@lab_test_ids,
        };
        my $flow_screen_data # arrayref:
			= $self->model('WorkList')->get_outstanding_investigations($args);

		# parse flow screen data for template (returns hashref or undef):
		if ( my $data = $self->_parse_flow_screen_data($flow_screen_data) ) {
			# get a list of unique request_ids
			my $unique_ids = $self->get_unique_request_ids($flow_screen_data);

			{ # get specimen_map for template:
				my $map = $self->specimen_map($unique_ids);
				$self->tt_params( specimen_map => $map );
			}
            { # request_options:
                my $map = $self->request_options_map($unique_ids);
                $self->tt_params( request_options_map => $map );
            }

			{ # get section notes for flow cytometry section:
				# stash section object for request_section_notes_map():
				$self->stash( lab_section => $lab_section );
				my $map = $self->request_section_notes_map($unique_ids);
				$self->tt_params( request_section_notes_map => $map );
			}
			{ # haematology data:
				my @requests = keys %$data; # warn Dumper \@requests;
				my $o = $self->model('Result')->get_multiple_haem(\@requests);
				for ( @$o ) { # warn Dumper $_->as_tree;
					my $lab_number = $_->lab_number; # 	warn Dumper $data;
					$data->{$lab_number}{haematology} = $_->as_tree;
				}
			}
			$self->tt_params( flow_screen_data => $data );
		}
	}

	# get unregistered data from pre_registration tables:
	my $cases = $self->model('Local')->get_unregistered_requests;
	if (@$cases) {
		$self->tt_params( unregistered_cases => $cases );

		my @prereg_specimen_ids;
		{ # get list of pre_registration_specimen.id's from $cases:
			for my $case (@$cases) { # warn Dumper $case->as_tree;
				my $pre_registration_specimen = $case->pre_registration_specimen;
				foreach my $reg_specimen (@$pre_registration_specimen) {
					push @prereg_specimen_ids, $reg_specimen->id;
				}
			} # warn Dumper \@prereg_specimen_ids;
		}

		# get map of lab_tests for unregistered requests (if any):
        if (@prereg_specimen_ids) {
            my $lab_tests_map = $self->model('Local')
                ->get_unregistered_request_lab_tests(\@prereg_specimen_ids);
            $self->tt_params( unregistered_request_lab_tests => $lab_tests_map );
            # warn Dumper $lab_tests_map;
        }
	}

	{ # lab_test status_options for this section:
		my $options = $self->get_status_options_for_select($lab_section->id);
		$self->tt_params( status_opts => $options );
	}

	return 1;
}

# ------------------------------------------------------------------------------
sub haem_data : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

    my @args = ('RequestHaematology', { query => [ status => 'default' ] } );
    my $data = $self->model('Base')->get_objects(@args);

	{ # haem data, converted from sysmex to real values:
		my @haem = map $_->as_tree(deflate => 0), @$data; # extract data as hashrefs

		# massage haem data - convert params from sysmex to real (far too slow in tt):
		$self->_parse_haem_data(\@haem); # also adds param_flags & param_fields for tt
		$self->tt_params( haem_data => \@haem );
	}
	{ # lab_number (nn_nnnnn) => request.id map:
		my @lab_numbers = map $_->lab_number, @$data; # warn Dumper \@lab_numbers;
		my $map = $self->model('Request')
			->get_request_id_from_lab_number(\@lab_numbers);
		$self->tt_params( requestId_map => $map );
	}
    return 1;
}

# ------------------------------------------------------------------------------
sub outreach_clinic_returns : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $id = $self->param('id');

	if ($id) { # update request_clinic_return table & redirect back to worklist:
		my $vars = $self->query->Vars; # warn Dumper $vars;
		$vars->{request_id} = $id; # warn Dumper $vars;

		my $rtn = $vars->{appointment_date} # just return error if no data submitted:
			? $self->model('Outreach')->update_clinic_appointment($vars) # rtn 0 OR $err
			: $self->messages('worklist')->{no_data_submitted};

		# any $rtn is an error, otherwise update success:
		my $msg = $rtn || $self->messages('action')->{edit_success};
		my $f = $rtn ? 'error' : 'info';
		$self->flash( $f => $msg );

		my $addr = 'local_worklist?function_name=outreach_clinic_returns';
		# this works as we arrived direct to rm, not via default() using function_name param:
		return $self->redirect( $self->query->url . '/' . $addr );
    }

	# get list of unreported cases which still require gross-description:
	my $requests = $self->model('Outreach')->get_outstanding_clinic_returns;
	$self->tt_params( requests => $requests );
	return 1;
}

# ------------------------------------------------------------------------------
sub gross_description : Runmode {
    my $self = shift; $self->_debug_path(); # not called directly

	my $id = $self->param('id');

	if ($id) { # update request_specimen_detail table & redirect back to worklist:
		my $vars = $self->query->Vars; # warn Dumper $vars;
		$vars->{request_id} = $id; # warn Dumper $vars;

		my $rtn = $vars->{gross_description} # just return error if no data submitted:
			? $self->model('Local')->update_gross_description($vars) # rtn 0 OR $err
			: $self->messages('worklist')->{no_data_submitted};

		# any $rtn is an error, otherwise update success:
		my $msg = $rtn || $self->messages('action')->{edit_success};
		my $f = $rtn ? 'error' : 'info';
		$self->flash( $f => $msg );

		my $addr = 'local_worklist?function_name=gross_description';
		# this works as we arrived direct to rm, not via default() using function_name param:
		return $self->redirect( $self->query->url . '/' . $addr );
	}

	# get list of unreported cases which still require gross-description:
	my $requests = $self->model('Local')->get_outstanding_gross_description;
	$self->tt_params( requests => $requests );
	return 1;
}

# ------------------------------------------------------------------------------
sub histology_processing : Runmode {
    my $self = shift;  $self->_debug_path(); # not called directly

	# name of test for this worklist:
	my $test_name = 'cut_up';

	return $self->_format_lab_test_data($test_name);
}

# ------------------------------------------------------------------------------
sub histology_blocks : Runmode {
    my $self = shift;  $self->_debug_path(); # not called directly

	my $data = $self->model('WorkList')->get_outstanding_histology_blocks;
	{ # create hash of year => $data:
		my %h;
		for (@$data) {
			my $yr = $_->request->year;
			push @{ $h{$yr} }, $_;
		};
		$self->tt_params( requests => \%h );
	}

	# get a list of unique request_ids, return if empty:
	my $request_ids = $self->get_unique_request_ids($data); # warn Dumper $request_ids;
	return 0 unless @$request_ids;

	{ # get specimen_map for requests:
		my $specimen_map = $self->specimen_map($request_ids);
		$self->tt_params( specimen_map => $specimen_map );
	}
	{ # create map of request_id => block_ref for tmpl:
		my %block_refs = map { $_->request_id => $_->external_reference } @$data;
		$self->tt_params( block_refs_map => \%block_refs );
	}

	$self->csrf_insert_token; # prevent form resubmission

	return 1;
}

# ------------------------------------------------------------------------------
sub histology_staining : Runmode {
    my $self = shift;  $self->_debug_path(); # not called directly

	# name of test for this worklist:
	my $test_name = 'haematoxylin_eosin';

	return $self->_format_lab_test_data($test_name);
}

# ------------------------------------------------------------------------------
sub immunohistochemistry : Runmode {
    my $self = shift;  $self->_debug_path(); # not called directly

	# get list of lab_tests for immunohistochemistry secion:
	my %args = (
		section_name => 'Immunohistochemistry',
	);

	my $lab_tests = $self->model('LabTest')->get_section_lab_tests(\%args);

	my @lab_test_ids = map { $_->id } @$lab_tests;
	my @field_labels = map { $_->field_label } @$lab_tests;

	# get requests where test status is not complete:
	my $data = $self->model('WorkList')
		->get_outstanding_investigations({ lab_test_id => \@lab_test_ids });
	$self->tt_params( requests => $data );

	# get a list of unique request_ids, return if empty:
	my $request_ids = $self->get_unique_request_ids($data); # warn Dumper $request_ids;
	return 0 unless @$request_ids;

	{ # get specimen_map for requests:
		my $specimen_map = $self->specimen_map($request_ids);
		$self->tt_params( specimen_map => $specimen_map );
	}
	{ # request_options:
		my $map = $self->request_options_map($request_ids);
		$self->tt_params( request_options_map => $map );
	}

	{ # get lab_test history for tests:
		my %args = (
			request_ids => $request_ids,
			field_label => \@field_labels, # history table uses field label
		);
		my $lab_test_status_map
			= $self->lab_test_status_for_field_label_map(\%args);
		$self->tt_params( lab_test_status_map => $lab_test_status_map );
	}

	return 1;
}

# ------------------------------------------------------------------------------
sub fish_worksheets : Runmode {
    my $self = shift;  $self->_debug_path(); # not called directly

    # get lab_section object for FISH:
    my $lab_section =
        $self->model('LabSection')->get_lab_section_by_name('FISH');

    my $sort_order = $self->query->param('sort_by') || ''; # optional

    my %args = ( # includes possible args accepted by model method:
        lab_section_id => $lab_section->id,
        sort_by        => $sort_order,

        fetch_only => undef,
        lab_test_id => undef,
        lab_number_from => undef,
        status_option_id => undef,
    );

    my $data = $self->model('WorkList')->get_outstanding_investigations(\%args);
    $self->tt_params( data => $data );

    { # get some data maps for tmpl:
		my $unique_ids = $self->get_unique_request_ids($data); # arrayref of request_ids

		{ # specimens:
			my $map = $self->specimen_map($unique_ids);
			$self->tt_params( specimen_map => $map );
		}
		{ # request_options:
			my $map = $self->request_options_map($unique_ids);
			$self->tt_params( request_options_map => $map );
		}
    }

    return 1;
}

# ------------------------------------------------------------------------------
sub genomics_slf_cancer_tissue { shift->genomics_slf_requests('cancer_tissue') }
# ------------------------------------------------------------------------------
sub genomics_slf_cancer_blood { shift->genomics_slf_requests('cancer_blood')   }
# ------------------------------------------------------------------------------
sub genomics_slf_rare_disease { shift->genomics_slf_requests('rare_disease')   }

# ------------------------------------------------------------------------------
# common function for rare_disease, cancer_blood, cancer_tissue:
sub genomics_slf_requests {
    my $self = shift;  $self->_debug_path();
	my $type = shift; # rare_disease, cancer_blood, cancer_tissue

	my $data = $self->model('Local')->genomics_slf_requests($type);
	$self->tt_params(
		requests => $data,
		slf_type => $type,
	);
	$self->tt_name('worklist/local/genomics/slf_select.tt');
	return 1;
}

# ------------------------------------------------------------------------------
sub genomics_slf_data : Runmode {
    my $self = shift;  $self->_debug_path();

	my @request_ids  = $self->query->param('request_id'); # warn Dumper \@request_ids;
	unless (@request_ids) {
		my $msg = $self->messages('worklist')->{slf_no_request_ids};
		# my $addr = '/local_worklist?function_name=genomics_sample_linkage_select';
	    return $msg; # will open in new tab so just close it
	}

	my $slf_type = $self->query->param('slf_type'); # warn $slf_type;
	$self->tt_params( slf_type => $slf_type );

	my $data = $self->model('Local')->genomics_slf_data(\@request_ids);
	my $tmpl = 'worklist/local/genomics/sample_linkage_form_2d.tt';

	my $_self = $self; weaken $_self; # or get circular refs inside the callbacks
	my $barcode = sub {
		my $text = shift || return undef; # warn $text;
		if ($tmpl =~ /2d/) { # 2d barcode:
			my %args = ( css_class => 'hbc2d' );
			return $_self->barcode_data_matrix($text, %args); # excludes css
		}
		# 1d (linear) barcode:
		my %args = ( show_text => 0, bar_height => 25 );
		return $_self->barcode_code128($text, %args); # excludes css
	};
	$self->tt_params( render_barcode => $barcode );

	my $html;
	for my $req (@$data) { # warn Dumper $req;
		my $ref = $self->render_view($tmpl, { data => $req });
		$html .= $$ref; # de-refererence it 1st;
	} # warn $html;  return $html;
	{ # add css:
		my $css = $self->cfg->{path_to_www_docs}.'/css/local/genomics/slf.css';
		$self->add_webkit_stylesheet($css);
	}
	my $pdf = do {
		# landscape orientation, and apply 30mm bottom margin for linear barcodes to
		# prevent content under-spill (not for 2d barcodes but still need to supply value):
		my $margin_bottom = $tmpl =~ /2d/ ? '10mm' : '30mm'; # 10mm is default
		my %args = (
			orientation   => 'landscape',
			margin_bottom => $margin_bottom,
			margin_top    => '5mm',
		);
		$self->inline_html_to_pdf(\$html, %args);
	};
	$self->header_add(-type => 'application/pdf', -expires => 'now');
	return $pdf;
}

# ------------------------------------------------------------------------------
sub xna_stabilisation_worksheet {
    my $self = shift;  $self->_debug_path(); # not called directly

	# DNA & RNA extraction:
	my %args = (
		section  => 'Molecular',
		lab_test => [ qw(dna_extraction rna_extraction) ],
		status   => 'new', # status to get
	);
	return $self->_xna_extraction(\%args);
}

# ------------------------------------------------------------------------------
sub dna_extraction_worksheet {
    my $self = shift;  $self->_debug_path();

	my %args = (
		section  => 'Molecular',
		lab_test => [ qw(dna_extraction) ],
		status   => 'stabilised', # status to get
	);
	$self->tt_params( extraction_type => 'dna' );
	return $self->_xna_extraction(\%args);
}

# ------------------------------------------------------------------------------
sub trial_dna_extraction_worksheet {
    my $self = shift;  $self->_debug_path();

	my %args = (
		section  => 'Clinical trials',
		lab_test => [ qw(trial_dna_extraction) ],
		status   => 'new', # status to get
	);
	$self->tt_params( extraction_type => 'dna' );
	$self->tt_name('worklist/local/dna_extraction_worksheet.tt'); # don't need new tt
	return $self->_xna_extraction(\%args);
}

# ------------------------------------------------------------------------------
sub rna_extraction_worksheet {
    my $self = shift;  $self->_debug_path();

	my %args = (
		section  => 'Molecular',
		lab_test => [ qw(rna_extraction) ],
		status   => 'stabilised', # status to get
	);
	$self->tt_params( extraction_type => 'rna' );
	return $self->_xna_extraction(\%args);
}

# ------------------------------------------------------------------------------
sub trial_rna_extraction_worksheet {
    my $self = shift;  $self->_debug_path();

	my %args = (
		section  => 'Clinical trials',
		lab_test => [ qw(trial_rna_extraction) ],
		status   => 'new', # status to get
	);
	$self->tt_params( extraction_type => 'rna' );
	$self->tt_name('worklist/local/rna_extraction_worksheet.tt'); # don't need new tt
	return $self->_xna_extraction(\%args);
}

# ------------------------------------------------------------------------------
sub trial_store_plasma {
    my $self = shift;  $self->_debug_path();

	my %args = (
		section  => 'Clinical trials',
		lab_test => [ qw(store_plasma) ],
		status   => 'new', # status to get
	);
	$self->tt_name('worklist/local/store_plasma_worksheet.tt');
	return $self->_xna_extraction(\%args); # uses same logic as XNA extraction
}

# ------------------------------------------------------------------------------
sub outreach_unreported { # redirect to main worklist url:
    my $self = shift;
    my $addr = '/worklist/request_status?status_query=unreported_outreach';
    $self->tt_name('worklist/local/outreach/request_status.tt'); # just needs to exist
    return $self->redirect( $self->query->url . $addr );
}

# ------------------------------------------------------------------------------
sub outreach_unauthorised { # redirect to main worklist url:
    my $self = shift;
    my $addr = '/worklist/request_status?status_query=unauthorised_outreach';
    $self->tt_name('worklist/local/outreach/request_status.tt'); # just needs to exist
    return $self->redirect( $self->query->url . $addr );
}

# ------------------------------------------------------------------------------
sub outreach_tests_complete { # redirect to main worklist url:
    my $self = shift;
    my $addr = '/worklist/request_status?status_query='
		. 'unreported_tests_complete_outreach';
    $self->tt_name('worklist/local/outreach/request_status.tt'); # just needs to exist
    return $self->redirect( $self->query->url . $addr );
}

# ------------------------------------------------------------------------------
# common method for xna_stabilisation_worksheet & d/rna_extraction_worksheets
sub _xna_extraction {
    my ($self, $args) = @_; $self->_debug_path();

	my $lab_test = $args->{lab_test}; # arrayref
	my $section  = $args->{section};
	my $function = $self->query->param('function_name');
	my $status   = $args->{status};

	# get lab-test id's corresponding to lab_test arrayref entries:
	my @lab_test_ids = do {
		my %args = ( section_name => $section );
		my $lab_tests = $self->model('LabTest')->get_section_lab_tests(\%args);

		my %map = map +($_->test_name => $_->id), @$lab_tests; # warn Dumper \%map;
		@map{@$lab_test}; # get lab-test id's from test_name's
	}; # warn Dumper \@lab_test_ids;

    # status options map (for 'stabilised'):
	my $status_option_map = $self->lab_test_status_options_map('description');

    my %args = ( # includes possible args accepted by model method:
        lab_number_from => undef,
        lab_section_id 	=> undef,
        lab_test_id 	=> \@lab_test_ids,
        fetch_only 		=> undef,
        sort_by        	=> undef, # default (lab number) is OK
        status_option_id => $status_option_map->{$status}->{id},
    );
	# skip any unwanted screened-as requests:
	if ( my $cfg = $self->get_yaml_file('worklist_cfg') ) { # warn Dumper $yaml;
		# check it's generating hashref or die (can't return $self->error here):
		die "worklist_cfg.yml doesn't return hashref" unless ref $cfg eq 'HASH';
		if ( my $skip = $cfg->{xna_extraction}->{skip_screens} ) {
			$args{query_args} = [
				'request.request_initial_screen.screen.description',
				{ ne => $skip }, # eg Gallium trial
			];
		}
	}

    my $data = $self->model('WorkList')->get_outstanding_investigations(\%args);
    $self->tt_params( requests => $data );

    { # get some data maps for tmpl:
		my $unique_ids = $self->get_unique_request_ids($data); # arrayref of request_ids
		return 1 unless @$unique_ids; # or next 2 blocks throw error:

		{
			my $specimen_map = $self->_xna_extraction_specimen_map($unique_ids);
			$self->tt_params( specimen_map => $specimen_map );
		}
		{ # request_options:
			my $map = $self->request_options_map($unique_ids);
			$self->tt_params( request_options_map => $map );
		}
		{ # section lab-tests
			my %args = (
				section_name => $section,
				test_type    => 'test',
				is_active    => 'yes',
			); # warn Dumper \%args;

			my $tests = $self->model('LabTest')->get_section_lab_tests(\%args);
			$self->tt_params( lab_tests => $tests );
		}
		# get map to restrict requests if specific lab tests selected:
		if ( my @test_ids = $self->query->param('lab_test_id') ) {
			# get requests with @lab_test_ids:
			my @args = ( request_id => $unique_ids, lab_test_id => \@test_ids);
			my $o = $self->model('Base')
				->get_objects('RequestLabTestStatus', { query => \@args } );
			my %h = map +($_->request_id => 1), @$o;
			$self->tt_params( restrict_request_map => \%h );

			{ # get test name(s):
				my $tests_map = $self->lab_tests_map;
				my @test_names = map $tests_map->{$_}, @test_ids; # warn Dumper \@test_names;
				$self->tt_params( test_names => \@test_names );
			}
		}

		$self->tt_params( # add some params for tt:
			function_name => $function,
			lab_section   => $section,
		);
    }
	return 1;
}

# ------------------------------------------------------------------------------
sub store_plasma_worksheet : Runmode {
    my $self = shift;  $self->_debug_path($self->get_current_runmode);

	my $vars = $self->query->Vars(); # warn Dumper $vars;

	my $function_name = $vars->{function_name} # trial_dna_extraction, rna_extraction, etc
    || return $self->error('no function name param submitted'); # warn $function_name;

    # get request_id's from request_specimen form param or session:
	my @params = $self->query->param('request_specimen'); # from query param, as array!!

    my $request_id = $self->_extract_request_specimen(\@params); # warn Dumper $request_id;
    unless (@$request_id) { # at least 1 submitted
		$self->flash( error => $self->messages('worklist')->{no_print_ids} );
        my $url = sprintf '%s/local_worklist?function_name=%s',
			$self->query->url(), $function_name;
        return $self->redirect($url);
    }
    { # get request & report data for request_ids:
		my %args = ( # to use existing method used by Search function
			search_constraints => { id => $request_id },
			args_for_search => {
				sort_by => [ qw(requests.year requests.request_number) ],
			},
		); # warn Dumper \%args;
		my $requests = $self->model('Request')->find_requests(\%args);
		$self->tt_params( requests => $requests ); # warn Dumper $requests;
	}
    { # get screening terms:
        my $o = $self->model('Screen')->get_initial_screens($request_id);
        # convert to hashref map for tt:
        my %map = map { $_->request_id => $_->screen->description } @$o;
        $self->tt_params( presentations => \%map ); # warn Dumper \%map;
    }
	# some params for .tt:
	$self->tt_params( function_name => $function_name );

	my $tt = 'worklist/local/trials/store_plasma.tt';
    return $self->render_view($tt);
}

# ------------------------------------------------------------------------------
sub xna_extraction_worksheet : Runmode {
    my $self = shift;  $self->_debug_path($self->get_current_runmode);

	my $vars = $self->query->Vars(); # warn Dumper $vars;

    my $extraction_type = $vars->{extraction_type} # DNA or RNA
    || return $self->error('no extraction type param submitted'); # warn $extraction_type;

	my $function_name = $vars->{function_name} # trial_dna_extraction, rna_extraction, etc
    || return $self->error('no function name param submitted'); # warn $function_name;

    my $lab_section = $vars->{lab_section} # molecular, Clinical trial, etc
    || return $self->error('no lab-section param submitted'); # warn $lab_section;

	# if redirect from dna extraction labels print, data is already in session:
	my $have_session_data = $vars->{print_labels};

    # get request_id's from request_specimen form param or session:
	my @params = $have_session_data # ie redirect from label print
		? @{ $self->session->param('dna_extraction_request_specimen') } # session
		: $self->query->param('request_specimen'); # from query param, as array!!

    my $request_id = $self->_extract_request_specimen(\@params); # warn Dumper $request_id;
    unless (@$request_id) { # at least 1 submitted
		$self->flash( error => $self->messages('worklist')->{no_print_ids} );
        my $url = sprintf '%s/local_worklist?function_name=%s',
			$self->query->url(), $function_name;
        return $self->redirect($url);
    }
    # save request_specimen param to session for print labels if DNA extraction:
    if ( $extraction_type eq 'dna' && ! $have_session_data ) { # unless already there
        my @params = $self->query->param('request_specimen'); # warn Dumper \@params;
        $self->session->param( dna_extraction_request_specimen => \@params );
    }

    { # get request & report data for request_ids:
		my %args = ( # to use existing method used by Search function
			search_constraints => { id => $request_id },
			args_for_search => {
				sort_by => [ qw(requests.year requests.request_number) ],
			},
		); # warn Dumper \%args;
		my $requests = $self->model('Request')->find_requests(\%args);
		$self->tt_params( requests => $requests ); # warn Dumper $requests;
	}
    { # get screening terms:
        my $o = $self->model('Screen')->get_initial_screens($request_id);
        # convert to hashref map for tt:
        my %map = map { $_->request_id => $_->screen->description } @$o;
        $self->tt_params( presentations => \%map ); # warn Dumper \%map;
    }
	# some params for .tt:
	$self->tt_params( function_name => $function_name );
	$self->tt_params( lab_section   => $lab_section   );

	# DNA extraction .tt same for clinical trial & molecular section, not so for RNA:
	$extraction_type = 'trial_rna'
		if lc $lab_section =~ 'trial' && lc $extraction_type eq 'rna'; # warn $extraction_type;
	my $tt = "worklist/local/molecular/${extraction_type}_extraction.tt";
    return $self->render_view($tt);
}

# ------------------------------------------------------------------------------
sub sequencing_worksheet : Runmode  {
    my $self = shift;  $self->_debug_path();

    my %args = (
        function => 'Sequencing',
        status   => 'PCR', # required lab-test status
    );
    return $self->_pcr_and_sequencing_worksheet(\%args);
}

# ------------------------------------------------------------------------------
sub pcr_worksheet : Runmode {
    my $self = shift;  $self->_debug_path();

    my %args = (
        function => 'PCR',
        status   => 'new', # required lab-test status
    );
    return $self->_pcr_and_sequencing_worksheet(\%args);
}

# ------------------------------------------------------------------------------
sub pcr_status_overview : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	if ( my @test_ids = $self->query->param('lab_test_id') ) {
		my $data = $self->model('Local')->pcr_status_overview(\@test_ids);
		$self->tt_params( incomplete_requests => $data );

		{ # get test name(s):
			my $tests_map = $self->lab_tests_map;
			my @test_names = map $tests_map->{$_}, @test_ids; # warn Dumper \@test_names;
			$self->tt_params( test_names => \@test_names );
		}
	}
	else {
		my $lab_tests = $self->_get_section_lab_tests('Molecular');
		$self->tt_params( lab_tests => $lab_tests );
	}
	return 1;
}

# ------------------------------------------------------------------------------
sub chimerism_worksheet : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	# get all molecular tests:
	my $lab_tests = $self->_get_section_lab_tests('Molecular');
    # get active chimerism lab-tests (eg CD3_chimerism, CD15_chimerism, etc):
	my @test_ids = map { $_->id } grep {
		$_->is_active eq 'yes' && $_->test_name =~ /chimerism/;
	} @$lab_tests; # warn Dumper \@test_ids;

    my $args = { lab_test_id => \@test_ids };
	my $o = $self->model('WorkList')->get_outstanding_investigations($args);

    my $unique_request_ids = do { # unique request_id's from request_lab_test_status object
        my @ids = map $_->request_id, @$o;
        LIMS::Local::Utils::get_unique_elements(\@ids);
    }; # warn Dumper $unique_request_ids;
    { # skip requests where dna-extraction status not 'extracted':
        # get dna_extraction test_id - there's only 1 but needs to be array:
        my @test_id = map { $_->id }
            grep { $_->test_name eq 'dna_extraction' } @$lab_tests;
		my %args = (
			request_id  => $unique_request_ids,
			lab_test_id => \@test_ids,
		); # warn Dumper \%args;
        # get dna-extraction status for requests (returns AoH - in case both dna & rna):
		my $dna_extraction_status = $self->_get_xna_extraction_status(\%args);

        my @data;
        REQ: for my $req (@$o) { # warn Dumper $req->as_tree;
            my $request_id = $req->request_id;
            # $dna_extraction_status values = array of 1 href (as we only asked for dna):
            my $ref = $dna_extraction_status->{$request_id}->[0]; # 1st (and only) aref
            next REQ unless $ref->{status} eq 'complete';
            push @data, $req;
        }
        $self->tt_params( requests => \@data );
    }

	{ # specimen map:
		my $specimen_map = $self->specimen_map($unique_request_ids);
		$self->tt_params( specimen_map => $specimen_map );
	}
	{ # request_options:
		my $map = $self->request_options_map($unique_request_ids);
		$self->tt_params( request_options_map => $map );
	}
}

# ------------------------------------------------------------------------------
sub outreach_pack_forms : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->get_packs_due_details;
	$self->tt_params( packs => $data );

    { # callback for blood-tube-type:
        my $_self = $self; weaken $_self;
        $self->tt_params( tube_type => sub { $_self->get_blood_tube_type(@_) } );
    }

    return 1;
}

# ------------------------------------------------------------------------------
sub outreach_pack_labels : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->pack_labels;
	$self->tt_params( addresses => $data );

    return 1;
}

# ------------------------------------------------------------------------------
# looks for outreach cases where no new sample received by return due date
sub outreach_outstanding : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->get_overdue_packs; # warn Dumper $data;
	$self->tt_params( requests => $data );

    return 1;
}

# ------------------------------------------------------------------------------
sub outreach_notifications : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data # use same model as outreach_outstanding() but include flag:
        = $self->model('Outreach')->get_overdue_packs({ notifications => 1 });
	$self->tt_params( requests => $data ); # warn Dumper $requests;

	# callback to extract GP surname (split $_[0] on space, return 1st element):
	my $referrer = sub { (split(' ', shift))[0] };
	$self->tt_params( get_referrer_surname => $referrer );

    return 1;
}

# ------------------------------------------------------------------------------
sub outreach_notification_dispatch : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);
	return $self->outreach_notifications(); # uses same data & tt params (except callback)
}

# ------------------------------------------------------------------------------
sub outreach_report_labels : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);
    return 1; # requires date input - function handled by Outreach controller
}

# ------------------------------------------------------------------------------
sub outreach_reports_to_issue : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->reports_to_issue;
	$self->tt_params( requests => $data );

	return 1;
}

# ------------------------------------------------------------------------------
sub outreach_pack_dispatch : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->get_packs_due_summary;
	$self->tt_params( packs => $data );

    return 1;
}

# ------------------------------------------------------------------------------
sub outreach_packs_future : Runmode {
    my $self = shift; $self->_debug_path($self->get_current_runmode);

	my $data = $self->model('Outreach')->get_packs_due_future;
	$self->tt_params( packs => $data );

    return 1;
}

# ------------------------------------------------------------------------------
sub _pcr_and_sequencing_worksheet { # used by sequencing_worksheet() & pcr_worksheet()
    my $self = shift;  $self->_debug_path();
    my $args = shift;

    my $function = $args->{function};
    my $status   = $args->{status};

    # set worklist name from 'function' arg:
    $self->tt_params( worklist_function => $function );

	# set tt name (override default set by runmode) - do BEFORE possible return:
    $self->tt_name('worklist/local/pcr_and_sequencing_worksheet.tt');

	# lab_test_id can be multi-select:
	my @test_ids = $self->query->param('lab_test_id'); # warn Dumper \@test_ids;

	if (@test_ids) { # get requests for status option = new PCR lab-test(s):
		my $option_id = do {
			my $map = $self->lab_test_status_options_map('description'); # warn Dumper $map;
			$map->{$status}->{id};
		};
		my $args = { lab_test_id => \@test_ids, status_option_id => $option_id };

		# add request.id's if supplied by form (for printing final list):
		if ( my @params = $self->query->param('request_specimen') ) {
            # extract request_id's from request_specimen form param:
            my $request_id = $self->_extract_request_specimen(\@params); # arrayref
			$args->{request_id} = $request_id;
		}

		my $o = $self->model('WorkList')->get_outstanding_investigations($args);
		$self->tt_params( requests => $o );

		{ # get test name(s):
			my $tests_map = $self->lab_tests_map;
			my @test_names = map $tests_map->{$_}, @test_ids; # warn Dumper \@test_names;
			$self->tt_params( test_names => \@test_names );
		}

		my @request_ids = do { # get unique request id.s:
			my %h = map +($_->request_id => 1), @$o;
			keys %h;
		}; # warn Dumper \@request_ids;
		return 0 if ! @request_ids; # no need to continue

		{ # specimen map:
			my $specimen_map = $self->specimen_map(\@request_ids);
			$self->tt_params( specimen_map => $specimen_map );
		}
        { # request_options:
            my $map = $self->request_options_map(\@request_ids);
            $self->tt_params( request_options_map => $map );
        }
		if ( $function eq 'PCR' ) { # dna/rna extraction status:
			my %args = (
				request_id  => \@request_ids,
				lab_test_id => \@test_ids,
			); # warn Dumper \%args;
            my $extraction_status = $self->_get_xna_extraction_status(\%args);
			$self->tt_params( extraction_status => $extraction_status );
		}
		# add lab test ids for tt to pass back as hidden fields:
		$self->tt_params( lab_test_ids => \@test_ids );

		# override tt_name to load a printable worksheet tmpl if flag passed:
		if ( $self->query->param('print_worksheet') ) {
            my $tt = 'worklist/local/molecular/pcr_and_sequencing_worksheet.tt';
			$self->tt_name($tt);
		}
	}
	else {
		my $lab_tests = $self->_get_section_lab_tests('Molecular');
		$self->tt_params( lab_tests => $lab_tests );
	}
	return 1;
}

# ------------------------------------------------------------------------------
sub _format_lab_test_data {
	my ($self, $test_name) = @_; $self->_debug_path();

	# get lab_test:
	my $lab_test = $self->get_lab_test_for_unique_test_name($test_name)
	|| 	# have to die as default() caller doesn't handle err rtn:
	die "test_name = '$test_name' either not found, or is not unique";

	# get requests where test status is not complete:
	my $data = $self->model('WorkList')
		->get_outstanding_investigations({ lab_test_id => $lab_test->id });
	$self->tt_params( requests => $data );

	# get a list of unique request_ids, return if empty:
	my $request_ids = $self->get_unique_request_ids($data); # warn Dumper $request_ids;
	return 0 unless @$request_ids;

	{ # get specimen_map for requests:
		my $specimen_map = $self->specimen_map($request_ids);
		$self->tt_params( specimen_map => $specimen_map );
	}
	{ # request_options:
		my $map = $self->request_options_map($request_ids);
		$self->tt_params( request_options_map => $map );
	}

	{ # get lab_test history for test:
		my %args = (
			request_ids => $request_ids,
			field_label => $lab_test->field_label, # history table uses field label
		);
		my $lab_test_status_map
			= $self->lab_test_status_for_field_label_map(\%args);
		$self->tt_params( lab_test_status_map => $lab_test_status_map );
	}

	{ # get test results:
		my %args = (
			request_id     => $request_ids,
			lab_section_id => $lab_test->lab_section_id,
		);
		my $results_map # may return empty, so default is empty hashref:
			= $self->get_lab_test_results_for_lab_section(\%args) || {};
		$self->tt_params( results_map => $results_map ); # warn Dumper $results_map;
	}

	return 1;
}

# get pieces_and_blocks results:
sub _pieces_and_blocks {
    my ($self, $unique_ids) = @_; # arrayref of request_ids

    my $all_results =
        $self->model('Result')->get_request_lab_test_results($unique_ids);

    my %h; # capture last numerical character of result eg 5ae(2), (1)AE:
    for my $r (@$all_results) {
        next unless $r->lab_test->test_name eq 'pieces_blocks';
        my $request_id = $r->request_id;
        my $result     = $r->result; # warn $result;
        $result =~ s/\D//g; # remove non-numerical chars # warn $result;
        $h{$request_id} = substr($result, -1); # last digit
    } # warn Dumper \%h;
    return \%h;
}

# get external_refs:
sub _external_refs {
    my ($self, $unique_ids) = @_; # arrayref of request_ids

    my %args = (  query => [ request_id => $unique_ids ] );
    my $o = $self->model('Base')->get_objects('RequestExternalRef', \%args);

    my $sum = sub { LIMS::Local::Utils::sum_list(@_) };

    my %h;
    for my $r(@$o) {
        my $request_id = $r->request_id;
        my $n = &$sum([ 0, $r->external_reference =~ /x\s?(\d+)p/ig ]);
            # warn Dumper [$r->external_reference, $n];
        $h{$request_id} = $n;
    }
    return \%h;
}

# ------------------------------------------------------------------------------
# require separate entries for xFU composite samples, and then multiply each
# specimen by number of blocks from pieces_blocks & external_ref data:
sub _xna_extraction_specimen_map {
	my ($self, $request_ids) = @_; # arrayref

	my $specimen_map = $self->specimen_map($request_ids); # warn Dumper $map;
    my $ext_ref_map  = $self->_external_refs($request_ids);
    my $blocks_map   = $self->_pieces_and_blocks($request_ids);

    while ( my ($request_id, $data) = each %$specimen_map ) {
        my @sample_code = @{ $data->{sample_code} }; # arrayref
		{ # separate xFU into xF & xU:
			my $str = join ',', @sample_code; # easiest to create a ...
			$str =~ s/(\w)FU/$1F,$1U/g; # temp string and substitute
			@sample_code = split ',', $str; # warn Dumper \@sample_code;
		}
        { # multiply xU & xF by number of blocks from pieces_blocks result:
            my $blocks = $blocks_map->{$request_id} || 1;
            if ( $blocks > 1 ) { # warn $blocks;
                my @expanded = map { # expands xU & xF by no. of blocks:
                    ($_) x ( /(F|U)$/ ? $blocks : 1 )
                } @sample_code; # warn Dumper [$blocks, \@expanded];
                @sample_code = @expanded;
            }
        }
        { # multiply xBL by number of blocks from external_ref entry:
            my $blocks = $ext_ref_map->{$request_id} || 1;
            if ( $blocks > 1 ) { # warn $blocks;
                my @expanded = map { # expands xBL by no. of blocks:
                    ($_) x ( /BL$/ ? $blocks : 1 )
                } @sample_code; # warn Dumper [$blocks, \@expanded];
                @sample_code = @expanded;
            }
        }
        # replace $d->{sample_code} with (possibly) expanded @sample_code:
		my @data_refs = ( $data->{sample_code}, \@sample_code );
        $data->{sample_code} = \@sample_code if
			LIMS::Local::Utils::array_diff_count(@data_refs);
    }
	return $specimen_map;
}

# ------------------------------------------------------------------------------
# shared between pcr_worksheet() & chimerism_worksheet():
sub _get_xna_extraction_status {
    my $self = shift;
    my $args = shift;

	my $o = $self->model('Local')->get_xna_extraction_status($args);

    my %h;
	for my $req (@$o) { # warn Dumper
		my $id = $req->id; # request.id
		# request_lab_tests_status is arrayref (1-2-many rel), even
		# though should only be dna OR rna extraction associated per test:
		my $test_status = $req->request_lab_tests_status; # arrayref
		TEST: for (@$test_status) { # warn Dumper $_->as_tree;
			my $test_name = $_->lab_test->test_name; # only want extractions:
			next TEST unless $test_name =~ /[dr]na_extraction\Z/;
			my %data = (
				test_name => $test_name,
				status    => $_->status->description,
			);
			push @{ $h{$id} }, \%data;
		};
	}
    return \%h;
}

# ------------------------------------------------------------------------------
# need labno, sample type, last_name, flow_details & array of lab-test data for
# flow screen section for each entry in $flow_data:
sub _parse_flow_screen_data {
    my ($self, $flow_screen_data) = @_; $self->_debug_path();

	my $data; # hashref to hold parsed flow screen data

	REQUEST: # foreach request in $flow_screen_data:
	for my $request( @$flow_screen_data ) {
		# create lab_number in '%02d_%05d' format:
		my $lab_number = sprintf '%02d_%05d',
			$request->request->year - 2000,
			$request->request->request_number;

		# get lab-test data:
		my %lab_test_data = (
			name   => $request->lab_test->test_name,
            user   => $request->user->as_tree,
			status => $request->status->description,
		);

		# if lab_tests attr exists from any previous loop, just add new lab-test data:
		if ( my $lab_test_data = $data->{$lab_number}->{lab_tests} ) {
			push @$lab_test_data, \%lab_test_data;
			next REQUEST;
		}
		# create arrayref structure for lab_test_data, for re-use in any future loop:
		$data->{$lab_number}->{lab_tests} = [ \%lab_test_data ];
		$data->{$lab_number}->{request_id} = $request->request->id;
		$data->{$lab_number}->{patient}
			= $request->request->patient_case->patient->as_tree;
	}

	return $data;
	# my @data = map { $_->as_tree(deflate => 0) } @$data; # preserve datetime
}

sub _parse_haem_data {
    my ($self, $data) = @_; # warn Dumper $data; # AoH

    my @fields = qw( wbc rbc hb plt hct mcv mch mchc lymph_percent lymph
        mixed_percent mixed neutr_percent neutr );

    my $flag = {}; # hashref of params with flags
    my $NULL = qr{[*0]000}; # *000 or 0000

    for my $d(@$data) {
        my $lab_number = $d->{lab_number};

        PARAM: for my $f(@fields) {
            my $flag_field = sprintf '%s_f', $f; # eg hb_f, wbc_f, mixed_f, etc
            # add row param to $flag if <param>_f > 0, or param value = *000 or 0000:
            $flag->{$lab_number}{$f}++ if $d->{$flag_field} || $d->{$f} =~ /^$NULL\Z/;
            next PARAM if $d->{$f} =~ /^$NULL\Z/; # don't calculate, just report param

            # adjust sysmex params to 'real' values:
            if ( $f eq 'rbc' ) {
                $d->{rbc} = sprintf '%.2f', $d->{rbc} / 100; # rbc to 2dp eg 0277 => 2.77
            }
            elsif ( grep $f eq $_, qw/hb plt mchc/ ) {
                $d->{$f} = $d->{$f} / 1; # convert to int eg 0080 => 80, 0277 => 277
            }
            else { # convert to 1dp eg 0080 => 8.0, 0277 => 27.7
                $d->{$f} = sprintf '%.1f', $d->{$f} / 10;
            }
        }
    } # warn Dumper \%flag;

    $self->tt_params(
        param_fields => \@fields,
        param_flags  => $flag,
    );
}

sub _get_section_lab_tests {
	my ($self, $section_name) = @_;

	my %query = (
        section_name => $section_name,
        test_type    => 'test', # or comment out if panels required
        is_active    => 'yes',
    );
    my $sort_by = 'field_label'; # optional

	my $data = $self->model('LabTest')->get_section_lab_tests(\%query, $sort_by);
	return $data;
}

# split request_specimen form param into request_id & specimen, return request_ids:
# shared between pcr_worksheet() & xna_extraction_worksheet()
sub _extract_request_specimen {
    my ($self, $params) = @_; # warn Dumper $params; # arrayref

    my %map;
    for (@$params) {
		# data in "request_id~specimen" format (request_specimen lacks 'id' col):
        my ($request_id, $specimen) = split '~';
        push @{ $map{$request_id} }, $specimen; # create array of specimens
    } # warn Dumper \%map;
    $self->tt_params( request_specimen_map => \%map );

    # extract (unique) request_id's:
    my @request_ids = keys %map;
    return \@request_ids;
}

1;