First version of samples reports generated in the backend

First version of samples reports generated in the backend

First version of samples reports generated in the backend

First version of samples reports generated in the backend

Gemfile

@@ -33,6 +33,7 @@ gem 'jbuilder', '~> 2.5'
 gem 'view_components', git: 'https://github.com/manastech/rails-view_components.git', branch: 'master'
 gem 'prawn'
 gem 'prawn-svg'
+gem 'prawn-table'
 
 # Authentication
 # gem 'bcrypt-ruby', '~> 3.1.2'

Gemfile.lock

@@ -375,6 +375,8 @@ GEM
       css_parser (~> 1.6)
       prawn (>= 0.11.1, < 3)
       rexml (~> 3.2)
+    prawn-table (0.2.2)
+      prawn (>= 1.3.0, < 3.0.0)
     premailer (1.12.1)
       addressable
       css_parser (>= 1.6.0)
@@ -662,6 +664,7 @@ DEPENDENCIES
   paranoia (< 2.5.0)
   prawn
   prawn-svg
+  prawn-table
   premailer-rails (< 1.10)
   pry-byebug (< 3.10.0)
   pry-rescue

app/assets/javascripts/components/samples_reports_bar_chart.js.jsx

@@ -122,7 +122,7 @@ var SamplesReportsBarChart = React.createClass({
                             x={x(d.label)+x.rangeBand()/2-1}
                             y={y(d[barVariable]) - error}
                             width={2}
-                            height={error*2} />
+                            height={error*2+1} />
                       <rect 
                             x={x(d.label)}
                             y={y(d[barVariable]) - error - 1}

app/assets/stylesheets/_charts.scss

@@ -17,7 +17,7 @@
   }
 
   .errorbar{
-    fill: $gray2;
+    fill: #BBBBBB;
     opacity: 1;
   }
 

app/controllers/samples_reports_controller.rb

@@ -3,6 +3,8 @@
 class SamplesReportsController < ApplicationController
   include SamplesReportsHelper
 
+  skip_before_action :verify_authenticity_token
+
   helper_method :boxes_data
   helper_method :available_institutions
   helper_method :confusion_matrix
@@ -66,26 +68,48 @@ def create
     end
   end
 
+  def print
+    # convert json param to hash
+    json_params = JSON.parse(params[:json])
+    samples_report = SamplesReport.find(json_params["id"])
+
+    return unless authorize_resource(samples_report, READ_SAMPLES_REPORT)
+
+    purpose = samples_report.samples[0].box.purpose
+
+    options = {
+      :samples_report => samples_report,
+      :purpose => purpose
+    }
+
+    if purpose == "Challenge"
+      options[:threshold] = json_params["threshold"].to_f
+      options[:auc] = json_params["auc"].to_f
+      options[:threshold_tpr] = json_params["threshold_tpr"].to_f
+      options[:threshold_fpr] = json_params["threshold_fpr"].to_f
+    else
+      options[:threshold] = 0.0
+    end
+
+    options[:confusion_matrix] = confusion_matrix(samples_report.samples, options[:threshold])
+
+    options[:measured_signal_svg] = json_params["measured_signal_svg"]
+    options[:specific_svg] = json_params["specific_svg"]
+
+    send_data NihReport.new(options).render,
+      filename: "#{samples_report.name}.pdf",
+      type: "application/pdf",
+      disposition: "inline"
+  end
 
   def show
     @samples_report = SamplesReport.find(params[:id])
     return unless authorize_resource(@samples_report, READ_SAMPLES_REPORT)
     @reports_data = measured_signal_data(@samples_report)
     @samples_without_results_count = @samples_report.samples.without_results.count
     @purpose = @samples_report.samples[0].box.purpose
-
-    if params[:display] == "pdf"
-      gon.samples_report_id = @samples_report.id
-      gon.samples_report_name = @samples_report.name
-      gon.purpose = @purpose
-      gon.threshold = params[:threshold]
-      gon.min_threshold = params[:minthreshold]
-      gon.max_threshold = params[:maxthreshold]
-      render "_pdf_report", layout: false
-    else
-      @max_signal = @reports_data.reduce(0) { |a, e| e[:max] > a ? e[:max] : a }
-      @can_delete = has_access?(@samples_report, DELETE_SAMPLES_REPORT)
-    end
+    @max_signal = @reports_data.reduce(0) { |a, e| e[:max] > a ? e[:max] : a }
+    @can_delete = has_access?(@samples_report, DELETE_SAMPLES_REPORT)
   end
 
   def delete

app/documents/nih_report.rb

@@ -0,0 +1,189 @@
+class NihReport < BasePdf
+  include SamplesReportsHelper
+
+  def initialize(options = {})
+    @samples_report = options[:samples_report]
+    @purpose = options[:purpose]
+    @confusion_matrix = options[:confusion_matrix]
+    @options = options
+  end
+
+  def document
+    @document ||= Prawn::Document.new(
+      top_margin: 30,
+      left_margin: 20,
+      right_margin: 20,
+      bottom_margin: 30,
+      page_size: [842, 595], # A4
+      print_scaling: :none
+    )
+  end
+
+  def setup
+    font_families.update("OpenSans" => {
+      normal: assets_path.join("fonts/OpenSans/OpenSans-Regular.ttf"),
+      bold: assets_path.join("fonts/OpenSans/OpenSans-Bold.ttf"),
+    })
+    font "OpenSans"
+    font_size 5.3
+    default_leading 0
+  end
+
+  def template
+    render_header
+    render_report_details
+    render_confussion_matrix
+    start_new_page
+    render_header
+    render_svg_plot(@options[:measured_signal_svg])
+    start_new_page
+    render_header
+    render_svg_plot(@options[:specific_svg])
+  end
+
+  def render
+    setup
+    template
+    document.render
+  end
+
+  protected
+
+  def render_header
+    bounding_box [bounds.left, bounds.top], width: bounds.right do
+      text "Report: #{@samples_report.name}", character_spacing: -0.07, size: 10, position: :right, color: "999999", indent_paragraphs: 600
+      move_down 3
+      text "Created at #{@samples_report.created_at.strftime(I18n.t('date.input_format.pattern'))}", character_spacing: -0.07, size: 10, position: :right, color: "999999", indent_paragraphs: 600
+      move_up 25
+      image assets_path.join("images/cdx-logo-bw.png"), width: 50, position: 540
+      move_down 30
+    end
+  end
+
+  def render_report_details
+
+    data = [
+      ["<b>Purpose</b>", @purpose],
+      ["<b>Samples</b>", "#{@samples_report.samples_report_samples.length} samples" + (@samples_report.samples.without_results.count > 0 ? "\n(#{@samples_report.samples.without_results.count} without results)" : "")],
+    ]
+
+    if @purpose == "LOD"
+      data << ["<b>LOB</b>", @samples_report.lob&.round(3)]
+      data << ["<b>LOD</b>", @samples_report.lod&.round(3)]
+    elsif @purpose == "Challenge"
+      data << ["<b>Threshold</b>", @options[:threshold]&.round(3)]
+      data << ["<b>Computed ROC AUC</b>", @options[:auc]&.round(3)]
+      data << ["<b>Threshold's TPR</b>", @options[:threshold_tpr]&.round(3)]
+      data << ["<b>Threshold's FPR</b>", @options[:threshold_fpr]&.round(3)]
+    end
+
+    # transpose data
+    data = data.transpose
+
+    text "Summary", size: 15, style: :bold, indent_paragraphs: 60
+    move_down 10
+
+    table data, position: :center, width: 650 do
+      cells.style do |cell|
+        cell.border_width = 10
+        cell.border_color = "FFFFFF"
+        cell.padding = 5
+        cell.size = 10
+        cell.inline_format = true 
+        cell.align = :center
+      end
+    end
+
+    move_down 30
+  end
+
+  def render_confussion_matrix
+    move_down 10
+    data = [
+      ["", "PREDICTED\nNEGATIVE", "PREDICTED\n POSITIVE", "TOTAL"],
+      [
+        "ACTUAL\nNEGATIVE", 
+        "<font size='18'>#{@confusion_matrix[:true_negative]}</font>\nTrue Negative",
+        "<font size='18'>#{@confusion_matrix[:false_positive]}</font>\nFalse Positive",
+        "<font size='18'>#{@confusion_matrix[:true_negative] + @confusion_matrix[:false_positive]}</font>\nActual Negative"
+      ],
+      [
+        "ACTUAL\nPOSITIVE",
+        "<font size='18'>#{@confusion_matrix[:false_negative]}</font>\nFalse Negative",
+        "<font size='18'>#{@confusion_matrix[:true_positive]}</font>\nTrue Positive",
+        "<font size='18'>#{@confusion_matrix[:false_negative] + @confusion_matrix[:true_positive]}</font>\nActual Positive"
+      ],
+      [
+        "TOTAL",
+        "<font size='18'>#{@confusion_matrix[:true_negative] + @confusion_matrix[:false_negative]}</font>\nPredicted Negative",
+        "<font size='18'>#{@confusion_matrix[:false_positive] + @confusion_matrix[:true_positive]}</font>\nPredicted Positive",
+        "<font size='18'>#{@confusion_matrix[:true_negative] + @confusion_matrix[:false_positive] + @confusion_matrix[:false_negative] + @confusion_matrix[:true_positive]}</font>\nTotal"
+      ],
+    ]
+
+    inside_colors = [
+      "FFFFFF", "FFFFFF", "FFFFFF", "FFFFFF",
+      "FFFFFF", "F0F0F0", "F0F0F0", "FFFFFF",
+      "FFFFFF", "F0F0F0", "F0F0F0", "FFFFFF",
+      "FFFFFF", "FFFFFF", "FFFFFF", "FFFFFF",
+    ]
+    text_colors = [
+      "666666", "666666", "666666", "666666",
+      "666666", "000000", "000000", "666666",
+      "666666", "000000", "000000", "666666",
+      "666666", "666666", "666666", "666666",
+    ]
+    text_rotate = [
+      0, 0, 0, 0,
+      90, 0, 0, 0,
+      90, 0, 0, 0,
+      90, 0, 0, 0,
+    ]
+    cell_widths = [
+      70, 200, 200, 100,
+      70, 200, 200, 100,
+      70, 200, 200, 100,
+      70, 200, 200, 100,
+    ]
+    cell_heights = [
+      40, 40, 40, 40,
+      70, 70, 70, 70,
+      70, 70, 70, 70,
+      50, 50, 50, 50,
+    ]
+
+    text "Confusion Matrix", size: 15, style: :bold, indent_paragraphs: 60
+    move_down 30
+
+    i=0
+    table data, position: :center do
+      cells.style do |cell|
+        cell.border_width = 10
+        cell.border_color = "FFFFFF"
+        cell.background_color = inside_colors[i]
+        cell.padding_left = 5
+        cell.padding_right = 5
+        cell.padding_top = 2
+        cell.padding_bottom = 2
+        cell.size = 10
+        cell.align = :center
+        cell.valign = :center
+        cell.text_color = text_colors[i]
+        cell.rotate = text_rotate[i]
+        cell.rotate_around = :center
+        cell.height = cell_heights[i]
+        cell.width = cell_widths[i]
+        cell.inline_format = true 
+        i+=1
+      end
+    end
+    @current_cursor = cursor
+
+    rounded_rectangle [0, @current_cursor + 50], 50, @current_cursor - cursor + 10, 10
+  end
+
+  def render_svg_plot(svg)
+    svg URI.unescape(svg), vposition: :center
+  end
+
+end