pubmed_api 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: ba519175eb78466e8030b06079e7269864b35a5c
+  metadata.gz: dd746c28ff6467d98cc9453f4099ebb3a51be2f5
+  data.tar.gz: 466279c7008a90605975055c48e1e011818b4ab8
 SHA512:
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+  data.tar.gz: 93b6be04e8817a988b8c710d35c22db2c606e98fa6834ef9f08af98b33191c8aba6e4b4779a2a05e0b157245aa9ccbeaa0b69ee327baadc1696a5a2890e3752f

data/lib/pubmed_api/parsers.rb

@@ -9,6 +9,7 @@ module PubmedAPI
   	  results = SearchResult.new
   	  results.pmids = []
   	  results.mesh_terms = []
+      results.phrases_not_found = []
 
   	  results.count = doc.xpath('/eSearchResult/Count').first.content.to_i
 
@@ -21,7 +22,9 @@ module PubmedAPI
   	  end
 
   	  doc.xpath('/eSearchResult/ErrorList/PhraseNotFound').each {|n| results.phrases_not_found << n.content }
-  	  results
+  	  
+
+      results
   	
     end
 

data/lib/pubmed_api/version.rb

@@ -1,3 +1,3 @@
 module PubmedAPI
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/lib/pubmed_api.rb

@@ -14,10 +14,10 @@ module PubmedAPI
                        :database => 'pubmed', #which database eq pubmed/nlmcatalog
                        :verb => 'search', #which API verb to use e.g. search/fetch
                        :email => '',
-                       :reldate => 90, #How far back shall we go in days 
+                       #:reldate => 90, #How far back shall we go in days 
                        :retmax => 100000,
                        :retstart => 0,
-                       :load_all_pmids => false }
+                       :load_all_pmids => true }
                      
 
     URI_TEMPLATE = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/e{verb}.fcgi?db={database}&tool={tool}&email={email}'+
@@ -86,7 +86,6 @@ module PubmedAPI
 
       #Maked the HTTP request and return the responce
       #TODO handle failures
-      #Log API calls?
       def make_api_request(options)
           url = expand_uri(URI_TEMPLATE, options)
           Nokogiri::XML( open url )
@@ -94,11 +93,10 @@ module PubmedAPI
 
     
       #Some journals have odd NLMIDs that need to be searched for rarther than accessed directly.
-      #TODO combine into single API request 
       def convert_odd_journal_ids(id)
         
         new_id = nil
-        results = search(id, {:database => 'nlmcatalog', :reldate => '100000'})
+        results = search(id, {:database => 'nlmcatalog'})
         if results.pmids.length ==1
           new_id = results.pmids[0]
         else
@@ -107,6 +105,23 @@ module PubmedAPI
         new_id.to_s
       end
 
+      
+      def get_journal_id_from_issn(issn)
+        
+        id = nil
+        term = issn + "[ISSN]+AND+ncbijournals[filter]"
+
+        results = search(term, {:database => 'nlmcatalog'})
+        if results.pmids.length ==1
+          id = results.pmids[0]
+        else
+          puts "failed to find " + issn.to_s
+        end
+        
+        id.to_s
+      end
+
+
       # 300ms minimum wait.
       def wait
         sleep WAIT_TIME 

data/spec/lib/pubmed_api_spec.rb

@@ -4,19 +4,25 @@ describe PubmedAPI do
 
 
   it "should perform a search" do
-    strucs = PubmedAPI::Interface.search("quantum physics", {:load_all_pmids => true, :reldate => 90})    
-    expect(strucs.length > 10)
+    results = PubmedAPI::Interface.search("quantum physics", {:reldate => 90})    
+    expect(results.pmids.length).to be > 10
+  end
+
+  it "should handle phrases not found" do
+    title = "Electron-Vibrational Coupling in the Fenna-Matthews-Olson Complex of Prosthecochloris a estuarii Determined by Temperature-Dependent Absorption and Fluorescence Line-Narrowing Measurements"
+    results = PubmedAPI::Interface.search( title, {:load_all_pmids => true})
+    expect(results.phrases_not_found).to eql(["estuarii"])
   end
 
   it "should make an API call" do
-  	options = PubmedAPI::Interface::DEFAULT_OPTIONS
-  	options.merge({:query => 'term=scrotum'})
-  	
-  	doc = PubmedAPI::Interface.make_api_request(options)
-    records = doc.xpath('./*/*')
+    options = PubmedAPI::Interface::DEFAULT_OPTIONS
+    options = options.merge({:query => 'term=scrotum'})
+
+    doc = PubmedAPI::Interface.make_api_request(options)
+    records = doc.xpath('/eSearchResult/IdList/Id')
     count = doc.xpath('/eSearchResult/Count').first.content.to_i
-    expect(count > 0 )
-    expect(records.length == count)
+    expect(count).to be > 0
+    expect(records.length).to eql(count)
   end 
   
 
@@ -25,8 +31,8 @@ describe PubmedAPI do
     title = "Completing the picture for the smallest eigenvalue of real Wishart matrices."
     strucs = PubmedAPI::Interface.fetch_papers([id])
     paper = strucs[0]
-    expect(paper.title.eql?(title))
-    expect(paper.pmid.eql?(id))
+    expect(paper.title).to eql(title)
+    expect(paper.pmid).to eql(id)
   end 
 
   it "should fetch a journal" do
@@ -34,13 +40,18 @@ describe PubmedAPI do
     title = 'Physical review letters.'
     strucs = PubmedAPI::Interface.fetch_journals([id])
     j = strucs[0]
-    expect(j.title_long.eql?(title))
-    expect(j.nlmid.eql?(id))
+    expect(j.title_long).to eql(title)
+    expect(j.nlmid).to eql(id)
   end 
  
   it "it should fix strange journal ids" do
-     fixed = PubmedAPI::Interface.convert_odd_journal_ids('16930290R')
-     expect( fixed.eql?('100381'))
+     fixed = PubmedAPI::Interface.convert_odd_journal_ids('19620690R')
+     expect(fixed).to eql('100381')
+  end
+
+  it "it should get journal id from issn" do
+     fixed = PubmedAPI::Interface.get_journal_id_from_issn('1361-6633')
+     expect(fixed).to eql('100381')
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pubmed_api
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Kieran Higgins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-28 00:00:00.000000000 Z
+date: 2015-05-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler