snpr/lib/tasks/dump_annotation.rake

# frozen_string_literal: true
require 'csv'
require 'zip'
namespace :snps do
  desc "Iterates over all SNPs, writes a CSV of annotation into public/"
  task :dump => :environment do
    readme = File.new("#{Rails.root}/tmp/readme.txt", "w")
    # get date
    readme.write("File created at: #{Time.now}\n")
    readme.write("PLOS data is licensed under Creative Commons Attribution.\nhttp://creativecommons.org/licenses/by/3.0/\nWebsite: http://api.plos.org\n")
    readme.write("Mendeley data is licensed under Create Commons Attribution.\nhttp://creativecommons.org/licenses/by/3.0/\nWebsite: http://apidocs.mendeley.com/\n")
    readme.write("SNPedia data is licensed under Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported.\nhttp://creativecommons.org/licenses/by-nc-sa/3.0/us/\nWebsite: http://snpedia.com/index.php/SNPedia:FAQ#Legal_.2F_Licensing\n")
    readme.write("Genome.gov data is in the public domain.\nWebsite: http://www.genome.gov/copyright.cfm\n")
    readme.write("Personal Genome Project is licensed under CC0.\nhttp://creativecommons.org/publicdomain/zero/1.0/\nWebsite: http://evidence.personalgenomes.org/about\n")
    readme.close()
    # dump mendeley
    CSV.open("#{Rails.root}/tmp/mendeley.csv", "wb") do |csv|
      csv << ["Name", "Position", "Chromosome", "Year", "First author", "Title", "DOI", "Open Access status", "Link"]
      MendeleyPaper.find_each do |m|
        first_author = m.first_author
        year = m.pub_year
        title = m.title
        doi = m.doi
        oa = m.open_access
        link = m.mendeley_url
        m.snps.each do |snp|
          position = snp.position.strip
          name = snp.name
          chrom = snp.chromosome
          csv << [name, position, chrom, year, first_author, title, doi, oa, link]
        end
      end
    end
    # dump snpedia
    CSV.open("#{Rails.root}/tmp/snpedia.csv", "wb") do |csv|
      csv << ["Name", "Position", "Chromosome", "Summary", "Link"]
      SnpediaPaper.find_each do |sn|
        summary = sn.summary
        link = sn.url
        sn.snps.each do |snp|
          position = snp.position.strip
          name = snp.name
          chrom = snp.chromosome
          csv << [name, position, chrom, summary, link]
        end
      end
    end
    # dump plos
    CSV.open("#{Rails.root}/tmp/plos.csv","wb") do |csv|
      csv << ["Name", "Position", "Chromosome", "Year", "First author", "Title", "DOI"]
      PlosPaper.find_each do |sp|
        first_author = sp.first_author
        title = sp.title
        doi = sp.doi
        year = sp.pub_date
        sp.snps.each do |snp|
          position = snp.position.strip
          name = snp.name
          chrom = snp.chromosome
          csv << [name, position, chrom, year, first_author, title, doi]
        end
      end
    end
    # dump pgp
    CSV.open("#{Rails.root}/tmp/pgp.csv", "wb") do |csv|
      csv << ["Name", "Position", "Chromosome", "Gene", "Qualified Impact", "Inheritance", "Summary", "Trait"]
      PgpAnnotation.find_each do |spg|
        gene = spg.gene
        impact = spg.qualified_impact
        inheritance = spg.inheritance
        summ = spg.summary
        trait = spg.trait
        snp = spg.snp
        position = snp.position.strip
        name = snp.name
        chrom = snp.chromosome
        csv << [name, position, chrom, gene, impact, inheritance, summ, trait]
      end
    end
    # dump genome_gov
    CSV.open("#{Rails.root}/tmp/genome_gov.csv", "wb") do |csv|
      csv << ["Name", "Position", "Chromosome", "First Author", "Title", "Pubmed link", "Year", "Journal", "Trait", "p-value", "p-value description", "Confidence Interval"]
      GenomeGovPaper.find_each do |gg|
        author = gg.first_author
        title = gg.title
        pubmed = gg.pubmed_link
        journal = gg.journal
        year = gg.pub_date
        trait = gg.trait
        pvalue = gg.pvalue
        pvalue_description = gg.pvalue_description
        conf = gg.confidence_interval
        gg.snps.each do |snp|
          position = snp.position.strip
          name = snp.name
          chrom = snp.chromosome
          csv << [name, position, chrom, author, title, pubmed, year, journal, trait, pvalue, pvalue_description, conf]
        end
      end
    end

    # get rid of old Zip
    if File.exist? "#{Rails.root}/public/data/annotation.zip"
      File.delete("#{Rails.root}/public/data/annotation.zip")
    end

    # now zip the CSVs and put the zip into /public
    Zip::File.open("#{Rails.root}/public/data/annotation.zip", Zip::File::CREATE) do |zipfile|
      zipfile.add("genome_gov.csv", "#{Rails.root}/tmp/genome_gov.csv")
      zipfile.add("readme.txt", "#{Rails.root}/tmp/readme.txt")
      zipfile.add("pgp.csv", "#{Rails.root}/tmp/pgp.csv")
      zipfile.add("mendeley.csv", "#{Rails.root}/tmp/mendeley.csv")
      zipfile.add("plos.csv", "#{Rails.root}/tmp/plos.csv")
      zipfile.add("snpedia.csv", "#{Rails.root}/tmp/snpedia.csv")
    end
    FileUtils.chmod(0665, "#{Rails.root}/public/data/annotation.zip")
    # delete the CSVs?
  end
end