Class: PubmedSearch

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

Constant Summary collapse

WAIT_TIME =

seconds

1
DEFAULT_OPTIONS = 
{:retmax => 100000,
:retstart => 0,
:tool => 'ruby-pubmed_search',
:email => '',
:load_all_pmids => false }

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#count ⇒ Object

The Count field returned by your search. If pmids < count, then you need to look at your retmax or try load_all_pmids



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# File 'lib/pubmed_search.rb', line 13

def count
  @count
end

#exploded_mesh_terms ⇒ Object

Get the list of MeSH terms that PubMed exploded. For more information on MeSH term explosion, see www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2651214#id443777



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# File 'lib/pubmed_search.rb', line 16

def exploded_mesh_terms
  @exploded_mesh_terms
end

#phrases_not_found ⇒ Object

Get the list of PhraseNotFound terms returned by your search



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# File 'lib/pubmed_search.rb', line 19

def phrases_not_found
  @phrases_not_found
end

#pmids ⇒ Object

Get the list of Pubmed IDs returned by this esearch as an Array of Numbers



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# File 'lib/pubmed_search.rb', line 10

def pmids
  @pmids
end

Class Method Details

.search(term, options = {}) ⇒ Object

Performs a search to PubMed via eUtils with the given term String, and returns a PubmedSearch object modeling the response.

Accepts a Hash of options. Valid options are

  • :retmax - Defaults to 100,000 which is the largest retmax that PubMed will honor.

  • :retstart - Defaults to 0. Set higher if you need to page through results. You shouldn’t need to do that manually, because of the load_all_pmids option

  • :tool - Defaults to ‘ruby-pubmed_search’, set to the name of your tool per EUtils parameters specs

  • :email - Defaults to ”, set to your email address per EUtils parameters specs

  • :load_all_pmids - Defaults to false. If this is set true, then search will continue sending eSearches with an increasing retstart until the list of pmids == count. For instance, an eSearch for “Mus musculus” will return ~951134 results, but the highest retmax allowable is 100000. With load_all_pmids set true, search will automatically perform 10 eSearches and return the entire list of pmids in one go.



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# File 'lib/pubmed_search.rb', line 39

def search(term, options={})
  options = DEFAULT_OPTIONS.merge(options)

  results = do_search(new, term, options)

  if options[:load_all_pmids]
    # Send off subsequent requests to load all the PMIDs, add them to the results
    (options[:retmax]..results.count).step(options[:retmax]) do |step|
      do_search(results, term, options.merge({:retstart => step}))
    end 
  end

  results
end

.skip_wait=(setting) ⇒ Object

Setting this to true will prevent PubmedSearch from pausing before sending requests to PubMed. This is a fantastic way to get yourself banned from eUtils.

I only use this for testing.



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# File 'lib/pubmed_search.rb', line 63

def skip_wait=(setting)
  @skip_wait = setting
end

.wait ⇒ Object

As of May 2009, PubMed requires a 300ms pause between eUtils calls. It used to be 3 seconds. PubmedSearch pauses for 1 second just to be on the safe side.



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# File 'lib/pubmed_search.rb', line 56

def wait
  sleep WAIT_TIME unless @skip_wait
end