pubmed_api 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +14 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +31 -0
- data/Rakefile +7 -0
- data/lib/pubmed_api/parsers.rb +163 -0
- data/lib/pubmed_api/version.rb +3 -0
- data/lib/pubmed_api.rb +125 -0
- data/pubmed_api.gemspec +26 -0
- data/spec/lib/pubmed_api_spec.rb +46 -0
- data/spec/spec_helper.rb +1 -0
- metadata +114 -0
checksums.yaml
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SHA1:
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metadata.gz: 69035040fd451f5846e90b7512f6d5b2e68253a6
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data.tar.gz: ba519175eb78466e8030b06079e7269864b35a5c
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SHA512:
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metadata.gz: 68e45eb159acc8ed52bd9bc0641e12a745bb692a4289903222c7e979ac3a8825d5ab94d237eae211b504c0ebf38e6c91cae760607348ac054dae3d7a764d1844
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data.tar.gz: dadc39958aab5210b494547cfad68ab00a43b790ab84ee9f5723c468865241c84c9c6b2205bedaa81e5abf8870d8a468dd7931ece13076ff5dc998df5c1f76fb
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data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2015 Kieran Higgins
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# PubmedApi
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'pubmed_api'
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```
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install pubmed_api
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it ( https://github.com/[my-github-username]/pubmed_api/fork )
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create a new Pull Request
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data/Rakefile
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module PubmedAPI
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class XMLParser
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SearchResult = Struct.new(:count, :pmids, :mesh_terms, :phrases_not_found)
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def parse_search(doc)
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results = SearchResult.new
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results.pmids = []
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results.mesh_terms = []
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results.count = doc.xpath('/eSearchResult/Count').first.content.to_i
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doc.xpath('/eSearchResult/IdList/Id').each {|n| results.pmids << n.content.to_i}
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doc.xpath('/eSearchResult/TranslationStack/TermSet/Term').each do |n|
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if n.content =~ /"(.*)"\[MeSH Terms\]/
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results.mesh_terms << $1
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end
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end
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doc.xpath('/eSearchResult/ErrorList/PhraseNotFound').each {|n| results.phrases_not_found << n.content }
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results
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end
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PaperStruct = Struct.new( :title, :abstract, :article_date, :pubmed_date, :date_appeared,
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:doi, :authors, :pmid, :nlmid, :journal, :complete, :url, :pdf_url)
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def parse_papers(papers_xml)
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results = []
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papers_xml.each do |paper|
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#check it's actually a paper
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if paper.xpath('/*/*').first.name().eql?('PubmedArticle')
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paper_output = PaperStruct.new
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paper_output.title = paper.at('ArticleTitle').text
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begin
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paper_output.abstract = paper.at('Abstract').text
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rescue NoMethodError
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end
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begin
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#Date in Y/M/D format
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article_date = Date.new( paper.at('ArticleDate/Year').text.to_i, paper.at('ArticleDate/Month').text.to_i, paper.at('ArticleDate/Day').text.to_i)
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paper_output.article_date = article_date
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rescue NoMethodError
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#puts "no date " + " " + paper.css('PMID').text + " " + paper.css('ArticleTitle').text
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paper_output.article_date = Date.new()
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end
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#Parse mutlitple PubMedPubDate dates
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dates = paper.css('PubMedPubDate')
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paper_output.pmid = parse_pmid(paper.css('PMID').text)
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pub_date = [0,0,0]
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dates.each do |node|
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if node.attributes["PubStatus"].to_s == "entrez"
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pub_date = Date.new( node.at('Year').text.to_i, node.at('Month').text.to_i, node.at('Day').text.to_i)
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paper_output.pubmed_date = pub_date
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paper_output.date_appeared = pub_date
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end
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end
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ids = paper.css('ArticleId')
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ids.each do |node|
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v = node.attributes["IdType"].to_s
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if v == 'doi'
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paper_output.doi = node.text
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end
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end
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#Extract the authors as friendly string for now...
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#TODO handle authors properly
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authors = paper.css('Author')
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auth_arr = parse_authors(authors)
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author_string = ''
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auth_arr.each do |a|
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author_string += a[1] + ' ' + a[2] +', '
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end
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#cut additional ', ' off end
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author_string = author_string[0..-3]
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paper_output.authors = author_string
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paper_output.nlmid = paper.css('NlmUniqueID').text
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results << paper_output
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end
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end
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return results
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end
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JournalStruct = Struct.new( :issn, :nlmid, :title_long, :title_short, :started,:frequency)
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def parse_journals(journals_xml)
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j_struc_arr = []
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journals_xml.each do |j|
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j_struc = JournalStruct.new(j.css('ISSN').text, j.css('NlmUniqueID').text, j.xpath('./TitleMain/Title').text,
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j.css('MedlineTA').text, j.css('PublicationFirstYear').text, j.css('Frequency').text)
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j_struc_arr << j_struc
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end
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j_struc_arr
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end
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def parse_pmid(pmid)
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pmid = pmid.gsub('.', '')
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if pmid.length > 8
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pmid = pmid[0,8]
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end
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pmid
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end
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AuthorStruct = Struct.new( :fore_name, :initials, :last_name)
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def parse_authors(authors)
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authors_output =[]
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authors.each do |node|
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author_arr = Array.new(3,"")
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if v = node.at_css('ForeName')
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author_arr[0] = v.text
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end
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if v = node.at_css('Initials')
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author_arr[1] = v.text
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end
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if v = node.at_css('LastName')
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author_arr[2] = v.text
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end
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authors_output << author_arr
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end
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return authors_output
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end
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end
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end
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data/lib/pubmed_api.rb
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require 'pubmed_api/version'
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require 'pubmed_api/parsers'
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require 'open-uri'
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require 'nokogiri'
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module PubmedAPI
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class Interface
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WAIT_TIME = 0.5 # seconds
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DEFAULT_OPTIONS = {:tool => 'ruby-pubmed-api',
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:database => 'pubmed', #which database eq pubmed/nlmcatalog
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:verb => 'search', #which API verb to use e.g. search/fetch
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:email => '',
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:reldate => 90, #How far back shall we go in days
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:retmax => 100000,
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:retstart => 0,
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:load_all_pmids => false }
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URI_TEMPLATE = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/e{verb}.fcgi?db={database}&tool={tool}&email={email}'+
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'&reldate={reldate}&retmax={retmax}&retstart={retstart}&{query}&rettype=fasta&retmode=xml'
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class << self
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def search(term, options={})
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options = DEFAULT_OPTIONS.merge(options)
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results = do_search(term, options)
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if options[:load_all_pmids]
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# Send off subsequent requests to load all the PMIDs, add them to the results
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(options[:retmax]..results.count).step(options[:retmax]) do |step|
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results.pmids << do_search(term, options.merge({:retstart => step})).pmids
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end
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end
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results
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end
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# Performs a search and parses the response
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def do_search(search_term, options)
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wait
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doc = make_api_request(options.merge({:query => 'term='+search_term}))
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parser = XMLParser.new
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parser.parse_search(doc)
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end
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def fetch_papers(ids)
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xml = fetch_records(ids, 'pubmed')
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parser = XMLParser.new
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parser.parse_papers(xml)
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end
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def fetch_journals(nlmids)
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#Change the ids of those wierd journals
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nlmids = nlmids.map { |e| ((e.include? 'R') ? convert_odd_journal_ids(e) : e ) }
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xml = fetch_records(nlmids, 'nlmcatalog')
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parser = XMLParser.new
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parser.parse_journals(xml)
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end
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def fetch_records(ids, database)
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xml_records = []
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options = DEFAULT_OPTIONS
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#dice array into reasonable length chunks for download
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n_length = 500
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# TODO paralellise?
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ids.each_slice(n_length) do |slice|
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#Turn string to something html friendly
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id_string = slice.join(",")
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doc = make_api_request(options.merge({:verb => 'fetch',:database => database, :query => 'id='+id_string}))
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records = doc.xpath('./*/*')
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xml_records << records
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end
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xml_records.flatten
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end
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#Maked the HTTP request and return the responce
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#TODO handle failures
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#Log API calls?
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def make_api_request(options)
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url = expand_uri(URI_TEMPLATE, options)
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Nokogiri::XML( open url )
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end
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#Some journals have odd NLMIDs that need to be searched for rarther than accessed directly.
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#TODO combine into single API request
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def convert_odd_journal_ids(id)
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new_id = nil
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results = search(id, {:database => 'nlmcatalog', :reldate => '100000'})
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if results.pmids.length ==1
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new_id = results.pmids[0]
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else
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puts "failed to convert " + id.to_s
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end
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new_id.to_s
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end
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# 300ms minimum wait.
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def wait
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sleep WAIT_TIME
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end
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private
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def expand_uri(uri, options)
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uri.gsub(/\{(.*?)\}/) { URI.encode( (options[$1] || options[$1.to_sym] || '').to_s ) rescue '' }
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end
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end
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end
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end
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data/pubmed_api.gemspec
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'pubmed_api/version'
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Gem::Specification.new do |spec|
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spec.name = "pubmed_api"
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spec.version = PubmedAPI::VERSION
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spec.authors = ["Kieran Higgins"]
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spec.email = ["kieran.higgins@gmail.com"]
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spec.summary = %q{A Ruby gem for downloading paper and journal information from Pubmed Entrez.}
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spec.description = %q{A Ruby gem for downloading paper and journal information from Pubmed Entrez.}
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spec.homepage = ""
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spec.license = "MIT"
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spec.files = `git ls-files -z`.split("\x0")
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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|
+
spec.add_development_dependency "bundler", "~> 1.7"
|
22
|
+
spec.add_development_dependency "rake", "~> 10.0"
|
23
|
+
spec.add_development_dependency "rspec"
|
24
|
+
spec.add_dependency "nokogiri"
|
25
|
+
|
26
|
+
end
|
@@ -0,0 +1,46 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe PubmedAPI do
|
4
|
+
|
5
|
+
|
6
|
+
it "should perform a search" do
|
7
|
+
strucs = PubmedAPI::Interface.search("quantum physics", {:load_all_pmids => true, :reldate => 90})
|
8
|
+
expect(strucs.length > 10)
|
9
|
+
end
|
10
|
+
|
11
|
+
it "should make an API call" do
|
12
|
+
options = PubmedAPI::Interface::DEFAULT_OPTIONS
|
13
|
+
options.merge({:query => 'term=scrotum'})
|
14
|
+
|
15
|
+
doc = PubmedAPI::Interface.make_api_request(options)
|
16
|
+
records = doc.xpath('./*/*')
|
17
|
+
count = doc.xpath('/eSearchResult/Count').first.content.to_i
|
18
|
+
expect(count > 0 )
|
19
|
+
expect(records.length == count)
|
20
|
+
end
|
21
|
+
|
22
|
+
|
23
|
+
it "should fetch a paper" do
|
24
|
+
id = '25554862'
|
25
|
+
title = "Completing the picture for the smallest eigenvalue of real Wishart matrices."
|
26
|
+
strucs = PubmedAPI::Interface.fetch_papers([id])
|
27
|
+
paper = strucs[0]
|
28
|
+
expect(paper.title.eql?(title))
|
29
|
+
expect(paper.pmid.eql?(id))
|
30
|
+
end
|
31
|
+
|
32
|
+
it "should fetch a journal" do
|
33
|
+
id = '0401141'
|
34
|
+
title = 'Physical review letters.'
|
35
|
+
strucs = PubmedAPI::Interface.fetch_journals([id])
|
36
|
+
j = strucs[0]
|
37
|
+
expect(j.title_long.eql?(title))
|
38
|
+
expect(j.nlmid.eql?(id))
|
39
|
+
end
|
40
|
+
|
41
|
+
it "it should fix strange journal ids" do
|
42
|
+
fixed = PubmedAPI::Interface.convert_odd_journal_ids('16930290R')
|
43
|
+
expect( fixed.eql?('100381'))
|
44
|
+
end
|
45
|
+
|
46
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
require 'pubmed_api'
|
metadata
ADDED
@@ -0,0 +1,114 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: pubmed_api
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Kieran Higgins
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2015-04-28 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.7'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.7'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '10.0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - "~>"
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '10.0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rspec
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ">="
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: nokogiri
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
description: A Ruby gem for downloading paper and journal information from Pubmed
|
70
|
+
Entrez.
|
71
|
+
email:
|
72
|
+
- kieran.higgins@gmail.com
|
73
|
+
executables: []
|
74
|
+
extensions: []
|
75
|
+
extra_rdoc_files: []
|
76
|
+
files:
|
77
|
+
- ".gitignore"
|
78
|
+
- Gemfile
|
79
|
+
- LICENSE.txt
|
80
|
+
- README.md
|
81
|
+
- Rakefile
|
82
|
+
- lib/pubmed_api.rb
|
83
|
+
- lib/pubmed_api/parsers.rb
|
84
|
+
- lib/pubmed_api/version.rb
|
85
|
+
- pubmed_api.gemspec
|
86
|
+
- spec/lib/pubmed_api_spec.rb
|
87
|
+
- spec/spec_helper.rb
|
88
|
+
homepage: ''
|
89
|
+
licenses:
|
90
|
+
- MIT
|
91
|
+
metadata: {}
|
92
|
+
post_install_message:
|
93
|
+
rdoc_options: []
|
94
|
+
require_paths:
|
95
|
+
- lib
|
96
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
97
|
+
requirements:
|
98
|
+
- - ">="
|
99
|
+
- !ruby/object:Gem::Version
|
100
|
+
version: '0'
|
101
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
102
|
+
requirements:
|
103
|
+
- - ">="
|
104
|
+
- !ruby/object:Gem::Version
|
105
|
+
version: '0'
|
106
|
+
requirements: []
|
107
|
+
rubyforge_project:
|
108
|
+
rubygems_version: 2.4.5
|
109
|
+
signing_key:
|
110
|
+
specification_version: 4
|
111
|
+
summary: A Ruby gem for downloading paper and journal information from Pubmed Entrez.
|
112
|
+
test_files:
|
113
|
+
- spec/lib/pubmed_api_spec.rb
|
114
|
+
- spec/spec_helper.rb
|