Class: ViralSeq::RecencyReport

Inherits:
Object
  • Object
show all
Defined in:
lib/viral_seq/recency_report.rb

Overview

class to generate recency report

Class Method Summary collapse

Class Method Details

.generate(log, outfile) ⇒ NilClass

to generate the recency report in .pdf format.

Parameters:

  • log (Hash) —

    Hash from the json summary string of the SDRM report

  • outfile (String) —

    path to the output file

Returns:

  • (NilClass) —

    .pdf file generated by the method. Return nil.



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# File 'lib/viral_seq/recency_report.rb', line 12

def self.generate(log, outfile)

  recency_color = {
    "recent" => "d42828",
    "chronic" => "0666bf",
    "indeterminant"=> "f78914",
    "insufficient data" => "7d7b79"
  }

  dual_infection_color = {
    "Yes" => "ffcc00",
    "No" => "339900",
    "insufficient data" => "7d7b79"
  }

  Prawn::Document.generate(outfile, margin: 75) do

    def text_format(text1, text2)
      [
        { text: text1 + "\s" * (30 - text1.size), styles: [:bold], size: 14, font: "Courier"},
        { text: text2, size: 14, styles: [:underline]}
      ]
    end

    def text_format2(text1, text2, text3, text4)
        text1 = text1.to_s
        text2 = text2.to_s
        text3 = text3.to_s
        text4 = text4.to_s

        [
          { text: "\s\s\s" + text1 + "\s"*(11-text1.size) +
        text2 + "\s"*(19-text2.size) +
        text3 + "\s"*(11-text3.size) + text4,
          size: 14,
          font: "Courier"
          }
        ]
    end

    text("Quantitative Recency Report by MPID-NGS",
    size: 18,
    align: :center,
    style: :bold
    )

    move_down 20

    formatted_text(
      text_format("Library ID:", log[:sample_id])
    )

    move_down 10

    formatted_text(
      text_format("ViralSeq Version:", ViralSeq::VERSION.to_s)

    )

    formatted_text(
      text_format("TCS Version:", ViralSeq::TCS_VERSION.to_s)
    )

    formatted_text(
      text_format("Processed Date", Time.now.strftime("%Y-%b-%d %H:%M"))
    )

    move_down 30

    text("Summary of parameters",
    size: 16,
    style: :bold
    )

    move_down 20

    formatted_text(
      [
        { text: "REGION" + "\s"*5 + "AVG. DIVERSITY" + "\s"*5 + "DIST20" + "\s"*5 + "DEPTH",
          styles: [:bold],
          size: 14,
          font: "Courier"
        },
      ]
    )

    move_down 5

    formatted_text(
      text_format2("RT", log[:pi_RT], log[:dist20_RT], log[:tcs_RT])
    )

    formatted_text(
      text_format2("V1V3", log[:pi_V1V3], log[:dist20_V1V3], log[:tcs_V1V3])
    )

    formatted_text(
      text_format2("P17", log[:pi_P17], log[:dist20_P17], log[:tcs_P17])
    )

    move_down 30

    formatted_text(
      [
        { text: "Prediction: ",
          styles: [:bold],
          size: 16,
        },

        { text: log[:recency].capitalize + " Infection",
          styles: [:bold],
          size: 16,
          color: recency_color[log[:recency]]
        },

        { text: " (9-month cutoff)",
          size: 14,
        },
      ]
    )

    move_down 20

    formatted_text(
      [
        {
          text: "Estimated Day Post Infection: ",
          styles: [:bold],
          size: 16
        },

        {
          text: log[:dpi].to_s +
          " (" + log[:dpi_lwr].to_s + "-" + log[:dpi_upr].to_s + ") Days",
          styles: [:bold],
          size: 16,
          color: recency_color[log[:recency]]
        }
      ]
    )

    move_down 20

    formatted_text(
      [
        {
          text: "Possible multivariant Infection: ",
          styles: [:bold],
          size: 16,
        },

        {
          text: log[:possible_dual_infection],
          styles: [:bold],
          size: 16,
          color: dual_infection_color[log[:possible_dual_infection]]
        }
      ]
    )

    move_down 10

    if log[:possible_dual_infection] == "Yes"

      formatted_text(
        [
          {
            text: "Warning: Days Post Infection prediction not reliable!",
            styles: [:bold],
            size: 14,
            color: "ffcc00"
          }
        ]
      )
    end
  end

end