entrez 0.4.0 → 0.5.0

data/README.rdoc

@@ -23,10 +23,10 @@ See 'Email & Tool' section below for setup.
 
 args:
 * database
-* params hash
+* params hash (optional)
 
   Entrez.EFetch('snp', id: 123, retmode: :xml)
-  #=> makes request to http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=9268480&retmode=xml
+  #=> makes request to http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=9268480&retmode=xml.
   #=> returns XML document with SNP rs9268480 data.
 
 ESummary takes the same arguments.
@@ -36,13 +36,23 @@ ESummary takes the same arguments.
 args:
 * database
 * term hash
-* params hash
+* params hash (optional)
 
   Entrez.ESearch('genomeprj', {WORD: 'hapmap', SEQS: 'inprogress'}, retmode: :xml)
-  #=> makes request to http://http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=genomeprj&term=hapmap[WORD]+AND+inprogress[SEQS]&retmode=xml
-  #=> returns XML document with list of Ids of genome projects that match the searc term criteria
+  #=> makes request to http://http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=genomeprj&term=hapmap[WORD]+AND+inprogress[SEQS]&retmode=xml.
+  #=> returns XML document with list of Ids of genome projects that match the searc term criteria.
   #=> i.e. genome projects that have 'hapmap' in the description and whose sequencing status is 'inprogress'.
 
+=== EInfo
+
+args:
+* database
+* params hash (optional)
+
+  Entrez.EInfo('gene', retmode: :xml)
+  #=> makes request to http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gene.
+  #=> returns XML document with list of searchable fields for gene database.
+
 == Email & Tool
 
 NCBI asks that you supply the tool you are using and your email.
@@ -63,7 +73,7 @@ The amount of delay time is no more than what is necessary to make the next requ
 * ESummary
 * ESearch
 
-Not yet implemented: EInfo, EPost, ELink, EGQuery, ESpell.
+Not yet implemented: EPost, ELink, EGQuery, ESpell.
 
 == Compatibility
 

data/lib/entrez.rb

@@ -10,19 +10,27 @@ class Entrez
 
   class << self
 
+    # E.g. Entrez.EFetch('snp', id: 123, retmode: :xml)
     def EFetch(db, params = {})
       perform '/efetch.fcgi', db, params
     end
 
-    def ESummary(db, params = {})
-      perform '/esummary.fcgi', db, params
+    # E.g. Entrez.EInfo('gene', retmode: :xml)
+    def EInfo(db, params = {})
+      perform '/einfo.fcgi', db, params
     end
 
+    # E.g. Entrez.ESearch('genomeprj', {WORD: 'hapmap', SEQS: 'inprogress'}, retmode: :xml)
     def ESearch(db, search_terms = {}, params = {})
       params[:term] = convert_search_term_hash(search_terms)
       perform '/esearch.fcgi', db, params
     end
 
+    # E.g. Entrez.ESummary('snp', id: 123, retmode: :xml)
+    def ESummary(db, params = {})
+      perform '/esummary.fcgi', db, params
+    end
+
     def perform(utility_path, db, params = {})
       respect_query_limit
       request_times << Time.now.to_f

data/lib/entrez/version.rb

@@ -1,3 +1,3 @@
 module Entrez
-  VERSION = "0.4.0"
+  VERSION = "0.5.0"
 end

data/spec/entrez_spec.rb

@@ -22,6 +22,11 @@ describe Entrez do
     response.body.should include('28911')
   end
 
+  it '#EInfo retrieves results' do
+    response = Entrez.EInfo('snp', retmode: :xml)
+    response.body.should include('<Name>RS</Name>')
+  end
+
   it 'should respect query limit' do
     requests = proc { 4.times { Entrez.EFetch('taxonomy', id: 9606) } }
     requests.should take_longer_than(1.0)

metadata

@@ -2,7 +2,7 @@
 name: entrez
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.4.0
+  version: 0.5.0
 platform: ruby
 authors: 
 - Jared Ning
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-19 00:00:00 -05:00
+date: 2011-05-28 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency