package LIMS::Controller::Chart; use Moose; BEGIN { extends 'LIMS::Base'; } with 'LIMS::Controller::Roles::Chart'; # contains ChartDirector chart methods use namespace::clean -except => 'meta'; __PACKAGE__->meta->make_immutable(inline_constructor => 0); use Regexp::Common qw(number); use LIMS::Local::Utils; use Data::Dumper; use lib '/home/raj/perl5/lib/perl5/ChartDirector'; use perlchartdir; perlchartdir::setLicenseCode('DEVP-2FRD-DL2X-7NGZ-2A94-4D2D'); # same as chartdir.lic # ------------------------------------------------------------------------------ sub default : StartRunmode { my $self = shift; $self->_debug_path($self->get_current_runmode); # redirect to /resources: return $self->redirect( $self->query->url . '/resources' ); } # ------------------------------------------------------------------------------ # just returns template, where name = param('id'): sub load : Runmode { my $self = shift; $self->_debug_path($self->get_current_runmode); my $template_name = $self->param('id') || $self->error( 'no template name passed to ' . $self->get_current_runmode ); { # make some useful dates available to templates: $self->tt_params( start_date => $self->model('Request')->get_first_request_date(), ); } my $template = 'chart/' . $template_name . '.tt'; $self->render_view($template); } # ------------------------------------------------------------------------------ # target for /chart/process// eg /chart/process/diagnoses/pie sub process : Runmode { my $self = shift; my $rm = $self->get_current_runmode; $self->_debug_path($rm); # get target method (eg diagnoses): my $target = $self->param('id') || $self->stash->{chart_method} || return $self->error( 'no target passed to ' . $rm ); # check it exists: unless ( $self->can($target) ) { return $self->error( "cannot find method for $target" ); } # get chart_type from 2nd token in $self->param my $chart_type = $self->param('Id') || $self->stash->{chart_type} || return $self->error( 'no chart type passed to ' . $rm ); # check it exists: unless ( $self->can($chart_type) ) { return $self->error( "cannot find method for $chart_type" ); } # create chart object in required method eg $self->diagnoses('pie_chart'): my $chart_obj = $self->$target($chart_type) || return $self->cleardot(); # or will get errors trying to parse non-existant data # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); # set header & return chart: $self->header_add(type => 'image/png'); return $chart; } # ------------------------------------------------------------------------------ sub hiv : Runmode { my $self = shift; # set header for png image: $self->header_add(type => 'image/png'); my %args = ( lab_section => 'Flow cytometry', presentation => 'HIV', # screened as ); my $data = $self->_get_param_monitoring_data(\%args) || return $self->cleardot(); my @chart_data; # create AoA: RESULT: for (@$data) { # AoH my $result = $_->{result}; my @date = split '-', $_->{date}; # split into components for chartTime() # initialise all vars to zero: my $CD4_total = 0; my ($CD4pos) = $result =~ /CD4\+ = (.*)\/uL/; # legacy my ($CD4posCD8neg) = $result =~ /CD4\+8\- T-cells = (.*) cells per microlitre/; my ($CD4posCD8pos) = $result =~ /CD4\+8\+ T-cells = (.*) cells per microlitre/; # make sure value not undef & remove any commas: map { $_ ||= 0; $_ =~ s/,//; # dat supplied as eg 1,234 } ($CD4pos, $CD4posCD8neg, $CD4posCD8pos); $CD4_total = $CD4posCD8neg + $CD4posCD8pos + $CD4pos; # skip unless have CD4 count: next RESULT unless $CD4_total; # warn Dumper $CD4_total; # add CD4 count & transformed date values: push @chart_data, [ $CD4_total, perlchartdir::chartTime(@date) ]; } # warn Dumper \@chart_data; # stash data for Roles::Chart::_get_chart_data(): $self->stash( chart_data => \@chart_data, chart_title => undef, # don't need one ); my $chart_obj = $self->plot_hiv(); # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); return $chart; } # ------------------------------------------------------------------------------ sub pnh : Runmode { my $self = shift; # set header for png image: $self->header_add(type => 'image/png'); my %args = ( lab_section => 'Flow cytometry', presentation => 'PNH', # screened as ); my $data = $self->_get_param_monitoring_data(\%args) || return $self->cleardot(); # warn Dumper $data; # integers & decimals: my $re = qr(\d+|\d+\.\d+|\d+\.|\.\d+); # eg 100 | 99.99 | 90. | .1 my @chart_data; # create AoA: RESULT: for (@$data) { # AoH my $result = $_->{result}; my @date = split '-', $_->{date}; # split into components for chartTime() my ($granulocyte_data) = $result =~ /Granulocyte PNH clone = ($re)%/; my ($erythrocyte_data) = $result =~ /Red cell PNH clone = ($re)%/; # warn Dumper [\@date, $granulocyte_data, $erythrocyte_data]; # skip unless have at least 1 result: next RESULT unless $granulocyte_data || $erythrocyte_data; # add granulocyte & red_cell clone data & transformed date values: my $pnh_data = [ $granulocyte_data, $erythrocyte_data ]; # deref'd in plot_pnh() push @chart_data, [ $pnh_data, perlchartdir::chartTime(@date) ]; } # warn Dumper \@chart_data; # stash data for Roles::Chart::_get_chart_data(): $self->stash( chart_data => \@chart_data, chart_title => undef, # don't need one ); my $chart_obj = $self->plot_pnh(); # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); return $chart; } # ------------------------------------------------------------------------------ sub outreach : Runmode { my $self = shift; # set header for png image: $self->header_add(type => 'image/png'); my $patient_id = $self->param('id'); # params to draw on chart: my @params = qw(hb plts creatinine paraprotein); # + calculated abnormal B cells: # for calculation of abnormal B cells: my @b_cell = qw(total_b_cells wbc neoplastic_b_cells); # get all request results for this patient: my $data = $self->model('Outreach')->get_chart_results( $patient_id, [ @params, @b_cell ] ); # create interim hash where keys = epoch seconds, vals = hashref of results: my %results = (); for (@$data) { # warn Dumper $_; my $result = $_->{result}; my $param = $_->{param_name}; my $date = $_->{created_at}; my $epoch = LIMS::Local::Utils::to_datetime_using_parsedate($date)->epoch; $results{$epoch}{$param} = $result; } # warn Dumper \%results; # create dataset for chart function: my @chart_data = (); for my $r ( sort keys %results ) { # $r = epoch seconds of requests.created_at my $data = $results{$r}; # results hashref for request my @results = map $data->{$_}, @params; # array of results for @params my $abnormal_b # calculate abnormal B cells from @b_cell param results: = $self->model('Outreach')->calculate_abnormal_bcells($data); push @results, $abnormal_b; # convert epoch back to DT for perlchartdir::chartTime(@date): my $dt = DateTime->from_epoch( epoch => $r ); my @date = ($dt->year, $dt->month, $dt->day); push @chart_data, [ \@results, perlchartdir::chartTime(@date) ]; } # warn Dumper \@chart_data; # stash data for Roles::Chart::_get_chart_data(): $self->stash( chart_data => \@chart_data, chart_title => undef, # don't need one ); my $chart_obj = $self->plot_outreach(); # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); return $chart; } # ------------------------------------------------------------------------------ sub outreach_param : Runmode { my $self = shift; # set header for png image: $self->header_add(type => 'image/png'); my $param = $self->param('id'); my $patient_id = $self->param('Id'); my $data = $self->model('Outreach')->get_chart_results( $patient_id, [ $param ] ); # warn Dumper $data; my (@chart_data, $field_label); for (@$data) { # warn Dumper $_; my $result = $_->{result}; my $date = $_->{created_at}; my $dt = LIMS::Local::Utils::to_datetime_using_parsedate($date); my @date = ($dt->year, $dt->month, $dt->day); # warn Dumper \@date; push @chart_data, [ $result, perlchartdir::chartTime(@date) ]; $field_label ||= $_->{field_label}; # all the same so 1st one will do } my $patient = $self->model('Patient')->get_patient($patient_id); my $title = sprintf '%s %s :: %s', ucfirst $patient->first_name, uc $patient->last_name, $field_label; # stash data for Roles::Chart::_get_chart_data(): $self->stash( chart_data => \@chart_data, chart_title => $title, ); my $chart_obj = $self->plot_outreach_param(); # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); return $chart; } # ------------------------------------------------------------------------------ sub imatinib : Runmode { my $self = shift; # set header for png image: $self->header_add(type => 'image/png'); my %args = ( lab_section => 'Molecular', presentation => 'CML imatinib PB follow-up', # screened as ); my $data = $self->_get_param_monitoring_data(\%args) || return $self->cleardot(); my @chart_data; # create AoA: RESULT: for (@$data) { # AoH my $result = $_->{result}; my @date = split '-', $_->{date}; # split into components for chartTime() my ($transcription_number) = $result =~ /transcription number = (\d+)/; my ($ratio) = $result =~ /BCR-ABL : ABL ratio = (.*)%/; # skip unless ratio result captured: next RESULT unless $ratio; # warn Dumper $ratio; # convert any 'less-than' result into real number: if ($ratio =~ /\A<(.*)/) { # set $transcription_number to zero (if not already): $transcription_number = 0; # changes plot symbol $ratio = $1; # remove leading '<' } # skip if still not 'real' number (ie integer or decimal): elsif ( $ratio !~ /\A$RE{num}{real}\Z/ ) { # warn $ratio; # $ratio = $perlchartdir::NoValue; # probably 'see comment' or 'failed' next RESULT; # so skip } # set point_type (depends whether transcription_number > 0): my $point_type = $transcription_number ? 1 : 0; # add ratio, transformed date values, and point_type: push @chart_data, [ $ratio, perlchartdir::chartTime(@date), $point_type ]; } # warn Dumper \@chart_data; # stash data for Roles::Chart::_get_chart_data(): $self->stash( chart_data => \@chart_data, chart_title => undef, # don't need one ); my $chart_obj = $self->plot_imatinib(); # send to finalise_chart() to add title (if required) & run makeChart2(): my $chart = $self->make_chart($chart_obj); return $chart; } # ------------------------------------------------------------------------------ # receives chart object, adds title (if required) & runs makeChart2(): sub make_chart { my $self = shift; my $chart = shift; # add a (optional) title to the chart: if ( my $title = $self->stash->{chart_title} ) { $chart->addTitle($title); } return $chart->makeChart2($perlchartdir::PNG); } # ------------------------------------------------------------------------------ sub diagnosis_status { my ($self, $chart_type) = @_; $self->_debug_path('diagnosis_status'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->get_diagnosis_status($vars); # $self->debug($data); # return 0 unless @$data; # doesn't cause problem if empty dataset # stash title & data for create_chart(): $self->stash( chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub diagnosis_frequency { my ($self, $chart_type) = @_; $self->_debug_path('diagnosis_frequency'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->get_diagnosis_frequency($vars); # $self->debug($data); return 0 unless @$data; # stash title & data for create_chart(): $self->stash( chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub specimen_frequency { my ($self, $chart_type) = @_; $self->_debug_path('diagnosis_frequency'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->get_specimen_frequency($vars); # $self->debug($data); return 0 unless @$data; # stash title & data for create_chart(): $self->stash( chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub new_diagnosis_frequency { my ($self, $chart_type) = @_; $self->_debug_path('diagnosis_frequency'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->get_new_diagnosis_frequency($vars); # $self->debug($data); return 0 unless @$data; # stash title & data for create_chart(): $self->stash( chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub presentation_frequency { my ($self, $chart_type) = @_; $self->_debug_path('presentation_frequency'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->get_presentation_frequency($vars); # $self->debug($data); return 0 unless @$data; # stash title & data for create_chart(): $self->stash( chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub requests_by_year { my ($self, $chart_type) = @_; $self->_debug_path('requests_by_year'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars); # supplied by template my $data = $self->model('Chart')->requests_by_year($vars); # $self->debug($data); # stash title & data for create_chart(): $self->stash( y_axis_label => 'requests', chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub requests_by_month { my ($self, $chart_type) = @_; $self->_debug_path('requests_by_month'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->requests_by_month($vars); # $self->debug($data); return 0 unless @$data; # stash title & data for create_chart(): $self->stash( y_axis_label => 'requests', chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub specimens_by_year { my ($self, $chart_type) = @_; $self->_debug_path('specimens_by_year'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars); # supplied by template my $data = $self->model('Chart')->specimens_by_year($vars); # $self->debug($data); # stash title & data for create_chart(): $self->stash( y_axis_label => 'specimens', chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub requests_by_day_of_week { my ($self, $chart_type) = @_; $self->_debug_path('requests_by_day_of_week'); my $vars = $self->query->Vars; # $self->debug($vars); my $title = $self->_get_chart_title($vars) || 'previous 365 days'; my $data = $self->model('Chart')->requests_by_day_of_week($vars); # $self->debug($data); # return 0 unless @$data; # doesn't cause problem if empty dataset # stash title,data & y_axis_label (if required) for create_chart(): $self->stash( y_axis_label => 'requests', chart_title => $title, chart_data => $data, ); my $chart = $self->$chart_type(); return $chart; } # ------------------------------------------------------------------------------ sub type_one { my $self = shift; $self->_debug_path($self->get_current_runmode); # The data for the pie chart my $data = [25, 18, 15, 12, 8, 30, 35]; # The labels for the pie chart my $labels = [ qw(CML DLBCL AML MDS CMPD Myeloma ALL) ]; # Create a PieChart object of size 360 x 300 pixels my $c = new PieChart(360, 300); # Set the center of the pie at (180, 140) and the radius to 100 pixels $c->setPieSize(180, 140, 100); # Add a title to the pie chart $c->addTitle('Diagnosis Frequency 2009'); # Draw the pie in 3D $c->set3D(); # Set the pie data and the pie labels $c->setData($data, $labels); # Explode the 1st sector (index = 0) $c->setExplode(0); return $c; } sub type_three { my $self = shift; # The data for the pie chart my $data = [13, 16, 42]; # The labels for the pie chart my $labels = [ qw(New Relapse FollowUp) ]; # The colors to use for the sectors my $colors = [0x66ff66, 0xff6666, 0xffff00]; # Create a PieChart object of size 300 x 300 pixels. Set the background to a gradient # color from blue (aaccff) to sky blue (ffffff), with a grey (888888) border. Use # rounded corners and soft drop shadow. my $c = new PieChart(300, 300); $c->setBackground($c->linearGradientColor(0, 0, 0, $c->getHeight() / 2, 0xaaccff, 0xffffff), 0x888888); $c->setRoundedFrame(); $c->setDropShadow(); if ( $self->query->param('foo') ) { #============================================================ # Draw a pie chart where the label is on top of the pie #============================================================ # Set the center of the pie at (150, 150) and the radius to 120 pixels $c->setPieSize(150, 150, 120); # Set the label position to -40 pixels from the perimeter of the pie (-ve means # label is inside the pie) $c->setLabelPos(-40); } else { #============================================================ # Draw a pie chart where the label is outside the pie #============================================================ # Set the center of the pie at (150, 150) and the radius to 80 pixels $c->setPieSize(150, 150, 80); # Set the sector label position to be 20 pixels from the pie. Use a join line to # connect the labels to the sectors. $c->setLabelPos(20, $perlchartdir::LineColor); } # Add a title to the pie chart $c->addTitle('Diagnosis Status 2009'); # Set the pie data and the pie labels $c->setData($data, $labels); # Set the sector colors $c->setColors2($perlchartdir::DataColor, $colors); # Use local gradient shading, with a 1 pixel semi-transparent black (bb000000) border $c->setSectorStyle($perlchartdir::LocalGradientShading, 0xbb000000, 1); return $c; } sub type_four { my $self = shift; # The value to display on the meter my $value = 27.48; # Create an AngularMeter object of size 200 x 115 pixels, with silver background # color, black border, 2 pixel 3D border border and rounded corners my $m = new AngularMeter(200, 115, perlchartdir::silverColor(), 0x000000, 2); $m->setRoundedFrame(); # Set the meter center at (100, 100), with radius 85 pixels, and span from -90 to +90 # degress (semi-circle) $m->setMeter(100, 100, 85, -90, 90); # Meter scale is 0 - 100, with major tick every 20 units, minor tick every 10 units, # and micro tick every 5 units $m->setScale(0, 100, 20, 10, 5); # Set 0 - 60 as green (66FF66) zone $m->addZone(0, 60, 0, 85, 0x66ff66); # Set 60 - 80 as yellow (FFFF33) zone $m->addZone(60, 80, 0, 85, 0xffff33); # Set 80 - 100 as red (FF6666) zone $m->addZone(80, 100, 0, 85, 0xff6666); # Add a text label centered at (100, 60) with 12 pts Arial Bold font $m->addText(100, 60, "Workload (% max)", "arialbd.ttf", 12, $perlchartdir::TextColor, $perlchartdir::Center); # Add a text box at the top right corner of the meter showing the value formatted to # 2 decimal places, using white text on a black background, and with 1 pixel 3D # depressed border $m->addText(156, 8, $m->formatValue($value, "2"), "arial.ttf", 8, 0xffffff )->setBackground(0x000000, 0, -1); # Add a semi-transparent blue (40666699) pointer with black border at the specified # value $m->addPointer($value, 0x40666699, 0x000000); return $m; } sub diagnosis { my $self = shift; my $d = $self->model('Chart')->get_diagnosis_frequency(); # $self->debug($d); # my (@terms, @count); # while ( my ($i, $term) = each %$d ) { # push @count, $i; # push @terms, $term; # } my @count = map $_->[0], @$d; my @terms = map $_->[1], @$d; # The data for the pie chart my $data = \@count; # The labels for the pie chart my $labels = \@terms; # Create a PieChart object of size 560 x 270 pixels, with a golden background and a 1 # pixel 3D border my $c = new PieChart(1000, 400, perlchartdir::goldColor(), -1, 1); # Add a title box using 15 pts Times Bold Italic font and metallic pink background # color $c->addTitle("Diagnosis Frequency 2009 (top 15)", "timesbi.ttf", 15) ->setBackground( perlchartdir::metalColor(0xff9999) ); # Set the center of the pie at (280, 135) and the radius to 110 pixels $c->setPieSize(500, 200, 150); # Draw the pie in 3D with 20 pixels 3D depth $c->set3D(20); # Use the side label layout method $c->setLabelLayout($perlchartdir::SideLayout); # Set the label box background color the same as the sector color, with glass effect, # and with 5 pixels rounded corners my $t = $c->setLabelStyle(); $t->setBackground($perlchartdir::SameAsMainColor, $perlchartdir::Transparent, perlchartdir::glassEffect()); #$t->setRoundedCorners(5); # Set the border color of the sector the same color as the fill color. Set the line # color of the join line to black (0x0) $c->setLineColor($perlchartdir::SameAsMainColor, 0x000000); # Set the start angle to 135 degrees may improve layout when there are many small # sectors at the end of the data array (that is, data sorted in descending order). It # is because this makes the small sectors position near the horizontal axis, where # the text label has the least tendency to overlap. For data sorted in ascending # order, a start angle of 45 degrees can be used instead. $c->setStartAngle(135); # Set the pie data and the pie labels $c->setData($data, $labels); return $c; } # ------------------------------------------------------------------------------ sub _get_param_monitoring_data { # eg HIV/Imatinib: my ($self, $args) = @_; # arrayref my $request_id = $self->param('id') # already checked in tmpl || return 0; my $request = $self->model('Request')->get_patient_and_request_data($request_id); # stash for later: $self->stash( request_data => $request->as_tree ); { # need at least 1 previous dataset to plot graph: my %h = ( request => $request, screen => $args->{presentation} ); # returns true if any previous data: $self->model('Local')->has_previous_data(\%h) || return 0; } { # get previous data on same patient: my $patient_id = $request->patient_case->patient_id; $args->{patient_id} = $patient_id; # add patient_id to args } my $data = $self->model('Chart')->get_param_monitoring_data($args); # $self->debug($data); return $data || 0; } # ------------------------------------------------------------------------------ sub _get_chart_title { my $self = shift; my $vars = shift; my $constraint_type = $vars->{constraint_type} || return; # undef on 1st call my $title; # uses same logic as Model::Chart::_get_search_constraints() to match search # constraints: if ($constraint_type eq 'all_data') { $title = 'all requests'; } elsif ($constraint_type eq 'this_year') { $title = 'year ' . DateTime->now->year; } elsif ( $constraint_type eq 'year_since' && $vars->{year} ) { # check var sent $title = "all from $vars->{year}"; } elsif ($vars->{days}) { $title = "previous $vars->{days} days" } elsif ($vars->{year}) { $title = "year $vars->{year}" } # ok to use $constraint_type as both dates validated before title set, if # invalid search constraints default to previous 365 days & default title used elsif ($constraint_type eq 'date_range') { # check they're both valid: my $start_date = LIMS::Local::Utils::check_date($vars->{date_from}); my $end_date = LIMS::Local::Utils::check_date($vars->{date_to}); # set title if both dates valid: if ($start_date && $end_date) { $title = "between $vars->{date_from} & $vars->{date_to}"; } } return $title; } 1;