mirror of
https://github.com/chenasraf/snpr.git
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7d0382b93c
* adds Open Humans connection (incl. at least some tests) * removes the capability to add fitbit data (was broken in any case) * display current fitbit data is still included, will be removed after grace period (needs to be announced to users)
90 lines
2.7 KiB
Ruby
90 lines
2.7 KiB
Ruby
# frozen_string_literal: true
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require "rubygems"
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require "net/http"
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require "json"
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class MendeleySearch
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include Sidekiq::Worker
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attr_reader :snp
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sidekiq_options queue: :mendeley, retry: 5, unique: true
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def perform(snp_id)
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return false # until OAuth2 implementation
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@snp = Snp.where(id: snp_id).first
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if snp.nil?
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logger.error("Snp(#{snp_id}) not found.")
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return
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end
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if update_mendeley?
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search
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else
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logger.info("mendeley papers for #{snp.name} do not need to be updated")
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end
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end
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def search
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page = 0
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items = 500
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begin
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result = Mendeley::API::Documents.
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search("\"#{snp.name}\"", { items: items, page: page })
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process_documents(result['documents'])
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page += 1
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sleep 1
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end while result['total_pages'].to_i.positive? &&
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result['total_pages'].to_i > result['current_page'].to_i
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snp.mendeley_updated = Time.now
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snp.ranking = snp.mendeley_papers.count +
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2 * snp.plos_papers.count + 5 * snp.snpedia_papers.count +
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2 * snp.genome_gov_papers.count + 2 * snp.pgp_annotations.count
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snp.save or raise(
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"could not save snp(#{snp.name}): #{snp.errors.full_messages.join(", ")}")
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if result["error"].present?
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logger.warn(
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"Mendeley API seems to be down.\nError is: #{result["error"]}")
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end
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end
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def process_documents(documents)
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if documents.blank?
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logger.info("mendeley: No papers found")
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return
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end
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documents.each do |document|
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uuid = document["uuid"].to_s
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mendeley_paper = MendeleyPaper.find_or_initialize_by(uuid: uuid)
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if mendeley_paper.new_record? || !mendeley_paper.valid?
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first_author = document["authors"].first
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if first_author.present?
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first_author = "#{first_author["forename"]} #{first_author["surname"]}"
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end
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logger.info("creating or updating paper")
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mendeley_paper.attributes = mendeley_paper.attributes.merge(
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title: document['title'],
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mendeley_url: document['mendeley_url'],
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first_author: first_author,
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pub_year: document['year'],
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uuid: uuid,
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doi: document["doi"].presence,
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)
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if !(mendeley_paper.valid? && mendeley_paper.save)
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logger.error("MendeleyPaper for #{snp.name} invalid.\n" <<
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mendeley_paper.errors.full_messages.join(", "))
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else
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mendeley_paper.snps << snp unless mendeley_paper.snps.include? snp
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end
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Sidekiq::Client.enqueue(MendeleyDetails, mendeley_paper.id)
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end
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end
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end
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def update_mendeley?
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(snp.mendeley_updated.nil? || snp.mendeley_updated < 31.days.ago) &&
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snp.name.index("vg").nil? && snp.name.index("mt-").nil?
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end
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end
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