pubmed_search 0.2.0 → 0.3.0

data/Rakefile

@@ -18,20 +18,20 @@ rescue LoadError
   puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
 end
 
-require 'spec/rake/spectask'
-Spec::Rake::SpecTask.new(:spec) do |spec|
-  spec.libs << 'lib' << 'spec'
-  spec.spec_files = FileList['spec/**/*_spec.rb']
-end
-
-Spec::Rake::SpecTask.new(:rcov) do |spec|
-  spec.libs << 'lib' << 'spec'
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.rcov = true
-end
-
-
-task :default => :spec
+# require 'spec/rake/spectask'
+# Spec::Rake::SpecTask.new(:spec) do |spec|
+#   spec.libs << 'lib' << 'spec'
+#   spec.spec_files = FileList['spec/**/*_spec.rb']
+# end
+# 
+# Spec::Rake::SpecTask.new(:rcov) do |spec|
+#   spec.libs << 'lib' << 'spec'
+#   spec.pattern = 'spec/**/*_spec.rb'
+#   spec.rcov = true
+# end
+# 
+# 
+# task :default => :spec
 
 require 'rake/rdoctask'
 Rake::RDocTask.new do |rdoc|

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.3.0

data/lib/pubmed_search.rb

@@ -22,9 +22,11 @@ class PubmedSearch
   WAIT_TIME = 1 # seconds
   DEFAULT_OPTIONS = {:retmax => 100000,
                      :retstart => 0,
+                     :tool => 'ruby-pubmed_search',
+                     :email => '',
                      :load_all_pmids => false }
                      
-  @uri_template = SimpleURITemplate.new('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax={retmax}&retstart={retstart}&term={term}')
+  @uri_template = SimpleURITemplate.new('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool={tool}&email={email}&retmax={retmax}&retstart={retstart}&term={term}')
   
   class << self
     # Performs a search to PubMed via eUtils with the given term +String+, and returns a +PubmedSearch+ object modeling the response.
@@ -32,6 +34,8 @@ class PubmedSearch
     # 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.
     def search(term, options={})
       options = DEFAULT_OPTIONS.merge(options)

data/pubmed_search.gemspec

@@ -1,54 +1,51 @@
 # Generated by jeweler
-# DO NOT EDIT THIS FILE
-# Instead, edit Jeweler::Tasks in Rakefile, and run `rake gemspec`
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
   s.name = %q{pubmed_search}
-  s.version = "0.2.0"
+  s.version = "0.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ryan Schenk"]
-  s.date = %q{2010-01-30}
+  s.date = %q{2010-12-13}
   s.email = %q{rschenk@gmail.com}
   s.extra_rdoc_files = [
     "LICENSE",
-     "README.rdoc"
+    "README.rdoc"
   ]
   s.files = [
     ".document",
-     ".gitignore",
-     "LICENSE",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "lib/pubmed_search.rb",
-     "pubmed_search.gemspec",
-     "spec/pubmed_search_spec.rb",
-     "spec/responses/bangana_tonkinensis_cranksection.xml",
-     "spec/responses/biodiversity_informatics.xml",
-     "spec/responses/e_coli_0.xml",
-     "spec/responses/e_coli_1.xml",
-     "spec/responses/e_coli_2.xml",
-     "spec/responses/mus_musculus.xml",
-     "spec/spec_helper.rb"
+    "LICENSE",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "lib/pubmed_search.rb",
+    "pubmed_search.gemspec",
+    "spec/pubmed_search_spec.rb",
+    "spec/responses/bangana_tonkinensis_cranksection.xml",
+    "spec/responses/biodiversity_informatics.xml",
+    "spec/responses/e_coli_0.xml",
+    "spec/responses/e_coli_1.xml",
+    "spec/responses/e_coli_2.xml",
+    "spec/responses/mus_musculus.xml",
+    "spec/spec_helper.rb"
   ]
-  s.has_rdoc = true
   s.homepage = %q{http://github.com/rschenk/pubmed_search}
-  s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.1}
+  s.rubygems_version = %q{1.3.7}
   s.summary = %q{A PubMed searching library with more features than BioRuby}
   s.test_files = [
     "spec/pubmed_search_spec.rb",
-     "spec/spec_helper.rb"
+    "spec/spec_helper.rb"
   ]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
-    s.specification_version = 2
+    s.specification_version = 3
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<rschenk-simple_uri_template>, [">= 0"])
       s.add_runtime_dependency(%q<nokogiri>, [">= 0"])
     else
@@ -60,3 +57,4 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<nokogiri>, [">= 0"])
   end
 end
+

data/spec/pubmed_search_spec.rb

@@ -44,10 +44,20 @@ describe PubmedSearch do
       FakeWeb.allow_net_connect = false
     end
     
+    it "should allow the user to specify the name of their tool" do
+      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ligercat&email=&retmax=100000&retstart=0&term=e%20coli",      :body => File.dirname(__FILE__) + '/responses/e_coli_0.xml')
+      PubmedSearch.search "e coli", :tool => 'ligercat' # note "tool=ligercat" in above URL. Fakeweb will complain and fail spec if necessary
+    end
+    
+    it "should allow the user to specify their email address" do
+      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ruby-pubmed_search&email=someone@someplace.edu&retmax=100000&retstart=0&term=e%20coli",      :body => File.dirname(__FILE__) + '/responses/e_coli_0.xml')
+      PubmedSearch.search "e coli", :email => 'someone@someplace.edu' # note "email=someone@someplace.edu" in above URL. Fakeweb will complain and fail spec if necessary
+    end
+    
     it "should allow multiple requests to NLM if Count > Retmax if desired" do
-      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100000&retstart=0&term=e%20coli",      :body => File.dirname(__FILE__) + '/responses/e_coli_0.xml')
-      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100000&retstart=100000&term=e%20coli", :body => File.dirname(__FILE__) + '/responses/e_coli_1.xml')
-      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100000&retstart=200000&term=e%20coli", :body => File.dirname(__FILE__) + '/responses/e_coli_2.xml')
+      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ruby-pubmed_search&email=&retmax=100000&retstart=0&term=e%20coli",      :body => File.dirname(__FILE__) + '/responses/e_coli_0.xml')
+      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ruby-pubmed_search&email=&retmax=100000&retstart=100000&term=e%20coli", :body => File.dirname(__FILE__) + '/responses/e_coli_1.xml')
+      FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ruby-pubmed_search&email=&retmax=100000&retstart=200000&term=e%20coli", :body => File.dirname(__FILE__) + '/responses/e_coli_2.xml')
             
       result = PubmedSearch.search("e coli", :load_all_pmids => true)
       

data/spec/spec_helper.rb

@@ -1,4 +1,5 @@
-require 'spec'
+require 'rubygems'
+require 'rspec'
 require 'uri'
 require 'fakeweb'
 
@@ -16,7 +17,7 @@ FakeWeb.allow_net_connect = false
 
 def fake_esearch_response(search_term, options={})
   file = options[:file] || search_term.downcase.gsub(/\W/, '_')
-  FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=100000&retstart=0&term=#{URI.escape search_term}",
+  FakeWeb.register_uri(:any, "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&tool=ruby-pubmed_search&email=&retmax=100000&retstart=0&term=#{URI.escape search_term}",
                        :body => File.dirname(__FILE__) + "/responses/#{file}.xml")
 end
 

metadata

@@ -1,7 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: pubmed_search
 version: !ruby/object:Gem::Version 
-  version: 0.2.0
+  hash: 19
+  prerelease: false
+  segments: 
+  - 0
+  - 3
+  - 0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Ryan Schenk
@@ -9,29 +15,37 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-30 00:00:00 -05:00
+date: 2010-12-13 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rschenk-simple_uri_template
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
         version: "0"
-    version: 
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: nokogiri
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
         version: "0"
-    version: 
+  type: :runtime
+  version_requirements: *id002
 description: 
 email: rschenk@gmail.com
 executables: []
@@ -43,7 +57,6 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .document
-- .gitignore
 - LICENSE
 - README.rdoc
 - Rakefile
@@ -63,28 +76,34 @@ homepage: http://github.com/rschenk/pubmed_search
 licenses: []
 
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.5
+rubygems_version: 1.3.7
 signing_key: 
-specification_version: 2
+specification_version: 3
 summary: A PubMed searching library with more features than BioRuby
 test_files: 
 - spec/pubmed_search_spec.rb

data/.gitignore

@@ -1,5 +0,0 @@
-*.sw?
-.DS_Store
-coverage
-rdoc
-pkg