dpickett-clinical 0.1.5 → 0.2.0

data/Rakefile

@@ -14,6 +14,7 @@ begin
     gem.add_dependency("jnunemaker-httparty", ">= 0.4.3")
     gem.add_dependency("jnunemaker-happymapper", ">= 0.2.5")
     gem.add_dependency("mislav-will_paginate", ">= 2.3.11")
+    gem.add_dependency("tenderlove-nokogiri", "> 1.3.3")
     
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.2.0

data/clinical.gemspec

@@ -2,11 +2,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{clinical}
-  s.version = "0.1.5"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan Pickett"]
-  s.date = %q{2009-07-02}
+  s.date = %q{2009-07-28}
   s.email = %q{dpickett@enlightsolutions.com}
   s.extra_rdoc_files = [
     "LICENSE",
@@ -21,6 +21,7 @@ Gem::Specification.new do |s|
      "VERSION",
      "clinical.gemspec",
      "features/finding_clinical_trials.feature",
+     "features/getting_keywords_and_categories.feature",
      "features/step_definitions/clinical_steps.rb",
      "features/support/env.rb",
      "lib/clinical.rb",
@@ -64,14 +65,17 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
       s.add_runtime_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
       s.add_runtime_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+      s.add_runtime_dependency(%q<tenderlove-nokogiri>, ["> 1.3.3"])
     else
       s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
       s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
       s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+      s.add_dependency(%q<tenderlove-nokogiri>, ["> 1.3.3"])
     end
   else
     s.add_dependency(%q<jnunemaker-httparty>, [">= 0.4.3"])
     s.add_dependency(%q<jnunemaker-happymapper>, [">= 0.2.5"])
     s.add_dependency(%q<mislav-will_paginate>, [">= 2.3.11"])
+    s.add_dependency(%q<tenderlove-nokogiri>, ["> 1.3.3"])
   end
 end

data/features/finding_clinical_trials.feature

@@ -49,3 +49,4 @@ Feature: As a potential participant for a clinical study
     When I attempt to retrieve trial "4325785"
     Then I should not get a trial
     
+

data/features/getting_keywords_and_categories.feature

@@ -0,0 +1,9 @@
+Feature: As a user of the clinical library
+  I want to retrieve keywords, categories, and terms from ClinicalTrials.gov
+  So that I can associate related trials
+
+  Scenario: Get keywords, categories, and terms
+    When I attempt to retrieve keywords for trial "NCT00001372"
+    Then the trial should have "keywords" like "Autoimmunity"
+    And the trial should have "categories" like "Urologic Diseases"
+    And the trial should have "terms" like "Connective Tissue Diseases"

data/features/step_definitions/clinical_steps.rb

@@ -22,6 +22,11 @@ When /^I attempt to retrieve trial "([^\"]*)"$/ do |id|
   @trial = Clinical::Trial.find_by_id(id)
 end
 
+When /^I attempt to retrieve keywords for trial "([^\"]*)"$/ do |id|
+  @trial = Clinical::Trial.find_by_id(id)
+  @trial.get_metadata
+end
+
 Then /^I should get trials that are (not )?"([^\"]*)"$/ do |not_included, field|
   if not_included
     result = false

data/lib/clinical.rb

@@ -3,6 +3,7 @@ $LOAD_PATH.unshift(File.dirname(__FILE__))
 require "will_paginate"
 require "httparty"
 require "happymapper"
+require "nokogiri"
 
 require "clinical/extensions"
 

data/lib/clinical/trial.rb

@@ -47,6 +47,10 @@ module Clinical
     element :brief_summary, String, :tag => "brief_summary/textblock"
     element :detailed_description, String, :tag => "brief_summary/textblock"
 
+    attr_reader :keywords
+    attr_reader :categories
+    attr_reader :terms
+
     def id
       self.nct_id
     end
@@ -79,6 +83,31 @@ module Clinical
       self.text_phase.gsub(/phase /i, "").to_i
     end
 
+    #this metadata is not accessible in the feed so crawl the html page
+    #to get keywords, categories, and terms
+    def get_metadata
+      response = self.class.get("/show/#{id}", :query => {:displayxml => false})
+      html = Nokogiri::HTML(response.body)
+
+      metadata = {}
+
+      {
+        :terms => 0, 
+        :categories => 1,
+        :keywords => 2
+      }.each do |key, value|
+
+        metadata[key] = []
+        html.search("div.indent3:nth-last-child(#{value}) td").each do |td|
+          metadata[key] += td.inner_html.split(/\<br\>/).collect{|i| i.strip}
+        end
+
+      end
+
+      @terms, @categories, @keywords = metadata[:terms], metadata[:categories], metadata[:keywords]
+      metadata
+    end
+
     class << self
       def find_by_id(id)
         response = get("/show/#{id}")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: dpickett-clinical
 version: !ruby/object:Gem::Version 
-  version: 0.1.5
+  version: 0.2.0
 platform: ruby
 authors: 
 - Dan Pickett
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-07-02 00:00:00 -07:00
+date: 2009-07-28 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -42,6 +42,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: 2.3.11
     version: 
+- !ruby/object:Gem::Dependency 
+  name: tenderlove-nokogiri
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">"
+      - !ruby/object:Gem::Version 
+        version: 1.3.3
+    version: 
 description: 
 email: dpickett@enlightsolutions.com
 executables: []
@@ -60,6 +70,7 @@ files:
 - VERSION
 - clinical.gemspec
 - features/finding_clinical_trials.feature
+- features/getting_keywords_and_categories.feature
 - features/step_definitions/clinical_steps.rb
 - features/support/env.rb
 - lib/clinical.rb
@@ -85,6 +96,7 @@ files:
 - test/test_helper.rb
 has_rdoc: true
 homepage: http://github.com/dpickett/clinical
+licenses: 
 post_install_message: 
 rdoc_options: 
 - --charset=UTF-8
@@ -105,7 +117,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.2.0
+rubygems_version: 1.3.5
 signing_key: 
 specification_version: 3
 summary: a library for accessing data from ClinicalTrials.gov