Class: Pubmedly::Client

Inherits:
Object
  • Object
show all
Defined in:
lib/pubmedly/client.rb

Overview

The Client class provides methods for accessing the NCBI’s eutils Pubmed API that return HTTP objects.

The NCBI eutils API provides access to many databases, but these out of the scope of pubmedly:

https://www.ncbi.nlm.nih.gov/books/NBK25497/table/chapter2.T._entrez_unique_identifiers_ui/?report=objectonly

Constant Summary collapse

BASE_URL = 
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
NCBI_DB = 
"pubmed"

Instance Method Summary collapse

Constructor Details

#initialize(api_key) ⇒ Client

Returns a new instance of Client.



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# File 'lib/pubmedly/client.rb', line 15

def initialize(api_key)
  @api_key = api_key
end

Instance Method Details

#fetch(*ids, **kwargs) ⇒ Object

www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch



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# File 'lib/pubmedly/client.rb', line 43

def fetch(*ids, **kwargs)
  url = URI.parse("#{BASE_URL}efetch.fcgi")

  params = kwargs.merge(
    db:      NCBI_DB,
    api_key: @api_key,
    id:      ids.join(",")
  )

  url.query = URI.encode_www_form(params)

  http         = Net::HTTP.new(url.host, url.port)
  http.use_ssl = true

  http.request(Net::HTTP::Get.new(url.request_uri))
end

#search(term, **kwargs) ⇒ Object

www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch For guidance on search terms: pubmed.ncbi.nlm.nih.gov/help/#how-do-i-search-pubmed To understand term mapping: pubmed.ncbi.nlm.nih.gov/help/#automatic-term-mapping List of all field tags: pubmed.ncbi.nlm.nih.gov/help/#search-tags Parameters for retrieval: www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch datetype parameter options: dataguide.nlm.nih.gov/eutilities/utilities.html#esearch-date-filter-parameters



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# File 'lib/pubmedly/client.rb', line 25

def search(term, **kwargs)
  url = URI.parse("#{BASE_URL}esearch.fcgi")

  params = kwargs.merge({
    db:      NCBI_DB,
    api_key: @api_key,
    term:    term,
  })

  url.query = URI.encode_www_form(params)

  http         = Net::HTTP.new(url.host, url.port)
  http.use_ssl = true

  http.request(Net::HTTP::Get.new(url.request_uri))
end