Class: Eutils

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

Overview

eutils.einfo

Constant Summary collapse

EUTILS_HOST =

Global constants

"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
EUTILS_INTERVAL = 
1.0 / 3.0
@@last_access = 
nil
@@last_access_mutex = 
nil

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(tool = nil, email = nil) ⇒ Eutils

Returns a new instance of Eutils.



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# File 'lib/eutils.rb', line 20

def initialize(tool = nil, email = nil)
  @tool, @email = tool, email
end

Instance Attribute Details

#email ⇒ Object

Returns the value of attribute email.



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# File 'lib/eutils.rb', line 17

def email
  @email
end

#tool ⇒ Object

Returns the value of attribute tool.



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# File 'lib/eutils.rb', line 17

def tool
  @tool
end

Instance Method Details

#efetch(db, webenv, query_key = 1, params = {}) ⇒ Object

EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user’s environment. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html



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# File 'lib/eutils.rb', line 77

def efetch(db, webenv, query_key = 1, params = {})
  params["db"] = db
  params["WebEnv"] = webenv
  params["query_key"] = query_key
  params["retmode"] ||= "xml"
  params["retstart"] ||= 0
  params["retmax"] ||= 10
  server = EUTILS_HOST + "efetch.fcgi"
  response = post_eutils(server, params)
  if params["retmode"] == "xml"
    return Hash.from_xml(response)
  else
    return response
  end
end

#egquery(term) ⇒ Object

EGQuery: Provides Entrez database counts in XML for a single search using Global Query. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/egquery_help.html



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# File 'lib/eutils.rb', line 112

def egquery(term)
  term.strip! if term.class == String
  #server = EUTILS_HOST + "egquery.fcgi"
  server = "http://eutils.ncbi.nlm.nih.gov/gquery/"
  params = {"term" => term, "retmode" => "xml"}
  response = post_eutils(server, params)
  return Hash.from_xml(response)["Result"]
end

#einfo(db = nil) ⇒ Object

EInfo: Provides field index term counts, last update, and available links for each database. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/einfo_help.html



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# File 'lib/eutils.rb', line 26

def einfo(db = nil)
  db.strip! if db.class == String
  server = EUTILS_HOST + "einfo.fcgi"
  params = {"db" => db}
  response = post_eutils(server, params)
  if db.nil? || db.empty?
    return response.scan(/<DbName>(\w+)<\/DbName>/).flatten
  else
    return Hash.from_xml(response)["eInfoResult"]
  end
end

#elink(ids, params = {}) ⇒ Object

ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html



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# File 'lib/eutils.rb', line 95

def elink(ids, params = {})
  params["id"] = ids.join(",")
  params["cmd"] ||= "neighbor"
  params["dbfrom"] ||= "pubmed"
  params["db"] ||= "pubmed"
  params["retmode"] ||= "xml"
  server = EUTILS_HOST + "elink.fcgi"
  response = post_eutils(server, params)
  if params["retmode"] == "xml"
    return Hash.from_xml(response)["eLinkResult"]
  else
    return response
  end
end

#epost(ids, db = "pubmed", params = {}) ⇒ Object

EPost: Posts a file containing a list of primary IDs for future use in the user’s environment to use with subsequent search strategies. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/epost_help.html returns: webenv, querykey. Both nil for invalid epost.



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# File 'lib/eutils.rb', line 54

def epost(ids, db = "pubmed", params = {})
  params["id"] = ids.join(",")
  params["db"] = db
  server = EUTILS_HOST + "epost.fcgi"
  response = post_eutils(server, params)
  querykey = response.scan(/<QueryKey>(\d+)<\/QueryKey>/).flatten.first.to_i
  querykey = nil if querykey == 0
  webenv = response.scan(/<WebEnv>(\S+)<\/WebEnv>/).flatten.first
  return webenv, querykey
end

#esearch(term, db = "pubmed", params = {}) ⇒ Object

ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user’s environment. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/esearch_help.html eutils.esearch(“autism”)



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# File 'lib/eutils.rb', line 41

def esearch(term, db = "pubmed", params = {})
  term.strip! if term.class == String
  params["term"] = term
  params["db"] = db
  params["usehistory"] ||= "y"
  server = EUTILS_HOST + "esearch.fcgi"
  response = post_eutils(server, params)
  return Hash.from_xml(response)["eSearchResult"]
end

#espell(term) ⇒ Object

ESpell: Retrieves spelling suggestions. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/espell_help.html



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# File 'lib/eutils.rb', line 123

def espell(term)
  term.strip! if term.class == String
  server = EUTILS_HOST + "espell.fcgi"
  params = {"db" => "pubmed", "term" => term}
  response = post_eutils(server, params)
  corrected = response.scan(/<CorrectedQuery>(.+)<\/CorrectedQuery>/).flatten.first.to_s
  corrected = term if corrected.empty?
  return corrected
end

#esummary(ids, db = "pubmed", params = {}) ⇒ Object

ESummary: Retrieves document summaries from a list of primary IDs or from the user’s environment. See also: eutils.ncbi.nlm.nih.gov/corehtml/query/static/esummary_help.html



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# File 'lib/eutils.rb', line 67

def esummary(ids, db = "pubmed", params = {})
  params["id"] = ids.join(",")
  params["db"] = db
  server = EUTILS_HOST + "esummary.fcgi"
  response = post_eutils(server, params)
  return Hash.from_xml(response)["eSummaryResult"]
end