mirror of
https://github.com/chenasraf/snpr.git
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906eef5403
* Passwords now need to be 8 characters long (new default in authlogic). * To login to the Sidekiq web interface, log in to opensnp.org, if you have the `admin` flag set, you will find it at the usual place. * I finally found out why Rubocop didn't complain about the frozen string literal pragma missing and added all of them. * Rubocop complained about keyword arguments, which is only relevant for Rails 5, so I disabled the cop. * I removed the `inherit_from: .rubocop_todo.yml` from `.rubocop.yml`, so Hound does complain about **all** the issues. I also added a few tasks for running Rubocop.
86 lines
2.4 KiB
Ruby
86 lines
2.4 KiB
Ruby
# frozen_string_literal: true
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# See http://api.plos.org/solr/faq/#solr_api_recommended_usage for API limits
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require 'plos'
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class PlosSearch
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include Sidekiq::Worker
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sidekiq_options queue: :plos, unique: true
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attr_reader :snp, :client
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def perform(snp_id)
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@snp = Snp.where(id: snp_id).first
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return false if @snp.nil? || snp_illegal? || recently_updated?
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@client = PLOS::Client.new(self.class.api_key)
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articles = perform_search
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# In many weird cases on production, articles is nil
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# (can't reproduce on development)
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# For now the workaround is to use Array.wrap to make empty list
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# i.e, nil => []
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# - Philipp
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Array.wrap(articles).each do |article|
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import_article(article) if not article.nil?
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end
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snp.plos_updated!
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logger.info('sleeping for 6 seconds in honor of the API limits')
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sleep(6)
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end
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def import_article(article)
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plos_paper_attributes = {
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first_author: article.try(:authors).try(:first).try(:to_s),
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doi: article.id,
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pub_date: article.published_at,
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title: article.title,
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}
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plos_paper = PlosPaper.find_or_initialize_by(doi: plos_paper_attributes[:doi])
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plos_paper.update_attributes!(plos_paper_attributes)
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plos_paper.snps << snp unless plos_paper.snps.include? snp
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Sidekiq::Client.enqueue(PlosDetails, plos_paper.id)
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end
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def perform_search
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# honoring API limits
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result = nil
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begin
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Timeout.timeout(5) do
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result = client.search(snp.name, 0, 999)
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end
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rescue Timeout::Error
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logger.error("API call timed out")
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false
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end
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logger.info('Successfully called the API')
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result
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# the following rescue never seems to fire? can't find the error in the logs - Philipp
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rescue => e
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logger.error("API call unsuccessful: Error was: #{e.class}: #{e.message}")
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raise e
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end
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def snp_illegal?
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# we don't need mitochondrial or VG-SNPs as these just result in noise
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# from the PLOS API
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forbidden_names = ["mt-", "vg"]
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if forbidden_names.any? { |part| snp.name[part] }
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logger.info("Snp #{snp.name} is a mitochondrial or vg snp")
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true
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else
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false
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end
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end
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def recently_updated?
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# we don't need to update snps that have been updated in the last month
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if snp.plos_updated > 31.days.ago
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logger.info("time threshold for #{snp.name} not met")
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true
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else
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false
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end
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end
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def self.api_key
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ENV.fetch('PLOS_API_KEY')
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end
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end
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