plos 0.0.3 → 0.0.4

data/README.md

@@ -20,16 +20,13 @@ Or install it yourself as:
 
 ### Searching
 
-You can perform a basic search using the ```PLOS::Client.search(query, rows, start)``` method. The second two parameters are optional. That method returns a ```PLOS::ArtcleSet``` object. ```ArticleSet``` inherits from Array and includes some meta-information about the search. The following example show the information that's available:
+You can perform a basic search using the ```PLOS::Client.search(query, start, rows)``` method. The second two parameters are optional. That method returns a ```PLOS::ArticleSet``` object. ```ArticleSet``` inherits from Array and includes some meta-information about the search. The following example show the information that's available:
 
 ```ruby
 require 'plos'
 
 client = PLOS::Client.new(ENV["API_KEY"])
 hits = client.search("xenograft")
-hits.each do |hit|
-  puts "#{hit.score} - #{hit.title} - #{hit.article_url}"
-end
 
 hits.status # Return status of the query (0 is success)
 hits.time # The amount of time the query took (in ms)
@@ -37,8 +34,9 @@ hits.num_found # Total number of results
 hits.max_score # Score of the closest matching document
 hits.start # Index of the first result
 
-xml = hits[2].article_xml
-puts hits[2].citation
+hits.each do |hit|
+  puts "#{hit.score} - #{hit.title} - #{hit.id}"
+end
 ```
 
 Change the number of results starting position. The following retrieves 50 results starting at result 100:
@@ -46,7 +44,7 @@ Change the number of results starting position. The following retrieves 50 resul
 ```ruby
 require 'plos'
 client = PLOS::Client.new(ENV["API_KEY"])
-hits = client.search("xenograft", 50, 100)
+hits = client.search("xenograft", 100, 50)
 ```
 
 Retrieve all results (paged). The following retrieves all results 200 - 300:
@@ -54,38 +52,39 @@ Retrieve all results (paged). The following retrieves all results 200 - 300:
 ```ruby
 require 'plos'
 client = PLOS::Client.new(ENV["API_KEY"])
-hits = client.all(100, 200)
+hits = client.all(200, 100)
 ```
 
 ### Getting the Article Details
 
-You can get the full article from the ```ArticleRef``` in a number of ways.
-
-You can get the raw xml content using ```ArticleRef.article_content```. For example, the following returns a string:
+You may get an ```Article``` object using ```ArticleRef.article```. For example, the following returns a ```PLOS::Article```:
 
 ```ruby
 require 'plos'
 client = PLOS::Client.new(ENV["API_KEY"])
 hits = client.search("xenograft")
-str = hits.first.article_content
+article = hits.first.article
 ```
 
-You may also get the parsed xml content using ```ArticleRef.article_xml```. For example, the following returns a ```Nokogiri::XML::Document```:
+### Getting the Article's Citation
+
+You may get a citation for the article using the ```citation``` method.
 
 ```ruby
 require 'plos'
 client = PLOS::Client.new(ENV["API_KEY"])
 hits = client.search("xenograft")
-xml_doc = hits.first.article_xml
+citation = hits.first.citation # returns the RIS citation for the first ArticleRef
 ```
 
-Finally you may get an ```Article``` object using ```ArticleRef.article```. For example, the following returns a ```PLOS::Article```:
+You may also get the citation from the ```Article``` object. The following code get the citation. Both ```Article```'s and ```ArticleRef```'s can return BibTex and RIS citations.
 
 ```ruby
 require 'plos'
 client = PLOS::Client.new(ENV["API_KEY"])
 hits = client.search("xenograft")
 article = hits.first.article
+citation = article.citation("bibtex") # returns the BibTex citation for the Article
 ```
 
 ### Working with Articles
@@ -113,6 +112,48 @@ article.sections      # Returns an Array of PLOS::Section objects containing the
 article.named_content # Returns an Array of Hash objects. Each representing a piece of "named-content". Named content is often used to separate genes from other text.
 ```
 
+### Other Helper Methods
+
+If you have the id of an ```Article```, you can get the content in various ways. You can get the raw content:
+
+```ruby
+require 'plos'
+client = PLOS::Client.new(ENV["API_KEY"])
+hits = client.search("xenograft")
+article_id = hits.first.id
+PLOS::Article.content(id) # Returns the xml as a string
+```
+
+```PLOS::Article.xml(id)``` returns a ```Nokogiri::XML``` object of the xml contents.
+
+```ruby
+require 'plos'
+client = PLOS::Client.new(ENV["API_KEY"])
+hits = client.search("xenograft")
+article_id = hits.first.id
+PLOS::Article.xml(article_id) # Returns the xml
+```
+
+```PLOS::Article.get(id)``` returns a ```PLOS::Article``` object.
+
+```ruby
+require 'plos'
+client = PLOS::Client.new(ENV["API_KEY"])
+hits = client.search("xenograft")
+article_id = hits.first.id
+PLOS::Article.get(article_id) # Returns the Article object
+```
+
+```PLOS::Article.citation(id)``` returns a ```PLOS::Article``` object.
+
+```ruby
+require 'plos'
+client = PLOS::Client.new(ENV["API_KEY"])
+hits = client.search("xenograft")
+article_id = hits.first.id
+PLOS::Article.citation(article_id) # Returns the RIS citation as a String (could pass "BibTex" as the second parameter to get the BibTex format)
+```
+
 ## Contributing
 
 1. Fork it

data/lib/plos/article.rb

@@ -2,6 +2,8 @@ module PLOS
   class Article
     include XmlHelpers
 
+    attr_accessor :node
+    attr_accessor :id
     attr_accessor :article_title
     attr_accessor :article_ids
     attr_accessor :journal_title
@@ -14,7 +16,10 @@ module PLOS
     attr_writer :sections
     attr_writer :named_content
 
-    def initialize(node)
+    def initialize(id, node)
+      self.id = id
+      self.node = node
+
       self.article_title = tag_value(node.search("title-group"), "article-title")
       self.journal_title = tag_value(node.search("journal-title-group"), "journal-title")
 
@@ -49,6 +54,40 @@ module PLOS
       end
     end
 
+    def self.base_url
+      "http://www.plosone.org"
+    end
+
+    def self.get(id)
+      PLOS::Article.new(id, self.xml(id))
+    end
+
+    def self.xml(id)
+      Nokogiri::XML(self.content(id))
+    end
+
+    def self.content(id)
+      RestClient.get(self.url(id))
+    end
+
+    def self.url(id, format="XML")
+      # format = "XML|PDF"
+      "#{base_url}/article/fetchObjectAttachment.action?uri=info:doi/#{id}&representation=#{format}"
+    end
+    
+    def self.ris_citation_url(id)
+      "#{base_url}/article/getRisCitation.action?articleURI=info:doi/#{id}"
+    end
+
+    def self.bib_tex_citation_url(id)
+      "#{base_url}/article/getBibTexCitation.action?articleURI=info:doi/#{id}"
+    end
+
+    def self.citation(id, format="RIS")
+      url = (format == "RIS" ? PLOS::Article.ris_citation_url(id) : PLOS::Article.bib_tex_citation_url(id))
+      RestClient.get(url)
+    end
+
     def authors
       contributors.collect { |contrib| contrib.name if contrib.type == "author" }.compact
     end
@@ -80,7 +119,9 @@ module PLOS
     def named_content
       @named_content ||= []
     end
+
+    def citation(format="RIS")
+      PLOS::Article.citation(id, format)
+    end
   end
 end
-
-# <named-content content-type="gene" xlink:type="simple">5′- AGGACGCAAGGAGGGTTTG -3′</named-content>

data/lib/plos/article_ref.rb

@@ -2,6 +2,7 @@ module PLOS
   class ArticleRef
     include PLOS::XmlHelpers
 
+    attr_accessor :node
     attr_accessor :client
     attr_accessor :score
     attr_accessor :type
@@ -18,6 +19,8 @@ module PLOS
     alias :publication_date= :published_at=
 
     def initialize(client, node)
+      self.node = node
+
       self.client = client
       node.children.each do |child|
         parse_node(child, self)
@@ -25,37 +28,11 @@ module PLOS
     end
 
     def article
-      @article ||= PLOS::Article.new(article_xml)
-    end
-
-    def article_xml
-      Nokogiri::XML(article_content)
-    end
-
-    def article_content
-      RestClient.get(article_url)
+      @article ||= PLOS::Article.get(id)
     end
 
     def citation(format="RIS")
-      url = (format == "RIS" ? ris_citation_url : bib_tex_citation_url)
-      RestClient.get(url)
-    end
-
-    def base_url
-      "http://www.plosone.org"
-    end
-
-    def article_url(format="XML")
-      # format = "XML|PDF"
-      "#{base_url}/article/fetchObjectAttachment.action?uri=info:doi/#{id}&representation=#{format}"
-    end
-    
-    def ris_citation_url
-      "#{base_url}/article/getRisCitation.action?articleURI=info:doi/#{id}"
-    end
-
-    def bib_tex_citation_url
-      "#{base_url}/article/getBibTexCitation.action?articleURI=info:doi/#{id}"
+      PLOS::Article.citation(id, format)
     end
   end
 end

data/lib/plos/client.rb

@@ -11,11 +11,11 @@ module PLOS
       self.base_url = base_url
     end
 
-    def all(rows=50, start=0)
+    def all(start=0, rows=50)
       search("*:*", rows, start)
     end
 
-    def search(query, rows=50, start=0)
+    def search(query, start=0, rows=50)
       result = PLOS::ArticleSet.new
       doc = execute( search_url, { :q => query, :rows => rows, :start => start } )
       if doc && doc.root

data/lib/plos/version.rb

@@ -1,3 +1,3 @@
 module Plos
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

data/spec/article1_spec.rb

@@ -2,7 +2,7 @@ require 'plos'
 
 describe PLOS do
   context "Article 1" do
-    let(:article) { PLOS::Article.new(Nokogiri::XML(File.read("spec/article1.xml"))) }
+    let(:article) { PLOS::Article.new("10.1371/journal.pone.0028384", Nokogiri::XML(File.read("spec/article1.xml"))) }
 
     it "should have the proper article title" do
       article.article_title.should == "Assessment of a Novel VEGF Targeted Agent Using Patient-Derived Tumor Tissue Xenograft Models of Colon Carcinoma with Lymphatic and Hepatic Metastases"

data/spec/article2_spec.rb

@@ -2,7 +2,7 @@ require 'plos'
 
 describe PLOS do
   context "Article 2" do
-    let(:article) { PLOS::Article.new(Nokogiri::XML(File.read("spec/article2.xml"))) }
+    let(:article) { PLOS::Article.new("10.1371/journal.pmed.0040075", Nokogiri::XML(File.read("spec/article2.xml"))) }
 
     it "should have the proper article title" do
       article.article_title.should == "Clinical Xenotransplantation of Organs: Why Aren't We There Yet?"

data/spec/plos_spec.rb

@@ -60,19 +60,19 @@ describe PLOS do
       end
 
       it "should have the proper xml article url" do
-        article.article_url.should == "http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0050494&representation=XML"
+        PLOS::Article.url(article.id).should == "http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0050494&representation=XML"
       end
 
       it "should have the proper pdf article url" do
-        article.article_url("PDF").should == "http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0050494&representation=PDF"
+        PLOS::Article.url(article.id, "PDF").should == "http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0050494&representation=PDF"
       end
 
       it "should have the proper ris citation url" do
-        article.ris_citation_url.should == "http://www.plosone.org/article/getRisCitation.action?articleURI=info:doi/10.1371/journal.pone.0050494"
+        PLOS::Article.ris_citation_url(article.id).should == "http://www.plosone.org/article/getRisCitation.action?articleURI=info:doi/10.1371/journal.pone.0050494"
       end
 
       it "should have the proper bib tex citation url" do
-        article.bib_tex_citation_url.should == "http://www.plosone.org/article/getBibTexCitation.action?articleURI=info:doi/10.1371/journal.pone.0050494"
+        PLOS::Article.bib_tex_citation_url(article.id).should == "http://www.plosone.org/article/getBibTexCitation.action?articleURI=info:doi/10.1371/journal.pone.0050494"
       end
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: plos
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-02-02 00:00:00.000000000 Z
+date: 2013-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -122,7 +122,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2041436036673742898
+      hash: -2910391070543665259
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -131,7 +131,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2041436036673742898
+      hash: -2910391070543665259
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24