oba-client 1.2.1 → 2.0.0

data/History.md

@@ -1,3 +1,7 @@
+## 2.0.0 / 2010-07-08
+
+* Parse XML entirely. See README for more information on the return value.
+
 ## 1.2.1 / 2010-07-08
 
 * Link correctly (problem with using markdown-ed URL in README.md).

data/README.md

@@ -33,9 +33,47 @@ See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Anno
     # Returns {:statistics  => {information about the annotation},
     #          :annotations => [Array of annotations of text],
     #          :ontologies  => [Array of ontologies used]}
+    # Like:
+    :statistics => {"MAPPING" => 1951, "MGREP" => 2319, "ISA_CLOSURE" => 30}
+    :annotations => [{
+      :score           => 199,
+      :id              => 203820,
+      :localConceptId  => "42877/CARO:0000013",
+      :localOntologyId => 42877,
+      :isTopLevel      => true,
+      :fullId          => "http://purl.obolibrary.org/obo/FBbt_00007002",
+      :preferredName   => "cell",
+      :synonyms        => ["body cell"],
+      :definitions     => ["a cell", "some other definition"],
+    	
+    	:semanticTypes => [
+    		{:id => 230820, :semanticType => "T043", :description => "desc"},
+    		"etc..."
+    	]
+    	
+    	:context => {
+    		:contextName   => "MAPPING",
+    		:isDirect      => false,
+    		:from          => 10,
+    		:to            => 20,
+    		:mappedConcept => {
+    			"has" => "the same information as other annotations, minus score"
+    	  }
+    	}
+    	
+      :mappingType => "Automatic"
+    }, "more annotations..."]
+    	
+    :ontologies => [{
+    	:localOntologyId   => 40404,
+    	:name	             => "Ontology Name",
+    	:virtualOntologyId => 1042
+    }, "more ontologies..."]
+    	
     client2.execute("another text string, maybe longer this time.")
     client2.execute("this is the second query for this client!")
     
+    
     # Or, parse some file you've already got lying about (pass as a string).
     parsed = OBAClient::parse("<?xml version='1.0'>...</xml>")
 

data/lib/oba_client.rb

@@ -5,7 +5,7 @@ require "net/http"
 require "uri"
 
 class OBAClient
-  VERSION = "1.2.1"
+  VERSION = "2.0.0"
 
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
   DEFAULT_TIMEOUT = 30
@@ -15,7 +15,7 @@ class OBAClient
 
   # The header for every request. There's no need to specify this per-instance.
   HEADER = {"Content-Type" => "application/x-www-form-urlencoded"}
-    
+
   # Parameters the annotator accepts. Any one not in this list (excluding
   # textToAnnotate) is not valid.
   ANNOTATOR_PARAMETERS = [
@@ -33,11 +33,11 @@ class OBAClient
     :scored,
     :semanticTypes,
     :stopWords,
-    :wholeWordOnly, 
+    :wholeWordOnly,
     :withDefaultStopWords,
     :withSynonyms,
   ]
-  
+
   STATISTICS_BEANS_XPATH = "/success/data/annotatorResultBean/statistics/statisticsBean"
   ANNOTATION_BEANS_XPATH = "/success/data/annotatorResultBean/annotations/annotationBean"
   ONTOLOGY_BEANS_XPATH =   "/success/data/annotatorResultBean/ontologies/ontologyUsedBean"
@@ -48,13 +48,24 @@ class OBAClient
   #   * [String] uri: the URI of the annotator service (default: {DEFAULT_URI}).
   #   * [Fixnum] timeout: the length of the read timeout (default: {DEFAULT_TIMEOUT}).
   #   * [Boolean] parse_xml: whether to parse the received text (default: false).
+  #   * [Array<String>] ontologies: a pseudo-parameter which will set both
+  #      ontologiesToExpand and ontologiesToKeepInResult.
   # @param [Hash<String, String>] options Parameters for the annotation.
   def initialize(options = {})
     @uri         = URI.parse(options.delete(:uri) || DEFAULT_URI)
     @timeout     = options.delete(:timeout)       || DEFAULT_TIMEOUT
     @parse_xml   = options.delete(:parse_xml)
-    
-    @options     = {}
+
+    if ontologies = options.delete(:ontologies)
+      [:ontologiesToExpand, :ontologiesToKeepInResult].each do |k|
+        if options.include?(k)
+          puts "WARNING: specified both :ontologies and #{k}, ignoring given value of #{k}."
+        end
+        options[k] = ontologies
+      end
+    end
+
+    @options = {}
     options.each do |k, v|
       if !ANNOTATOR_PARAMETERS.include?(k)
         puts "WARNING: #{k} is not a valid annotator parameter."
@@ -65,7 +76,7 @@ class OBAClient
         @options[k] = v
       end
     end
-    
+
     if !@options.include?(:email)
       puts "TIP: as a courtesy, consider including your email in the request."
     end
@@ -81,6 +92,7 @@ class OBAClient
     request.body = {:textToAnnotate => text}.merge(@options).map do |k, v|
       "#{CGI.escape(k.to_s)}=#{CGI.escape(v.to_s)}"
     end.join("&")
+    puts request.body if $DEBUG
 
     begin
       response = Net::HTTP.new(@uri.host, @uri.port).start do |http|
@@ -92,7 +104,7 @@ class OBAClient
       puts "Request for #{text[0..10]}... timed-out at #{@timeout} seconds."
     end
   end
-  
+
   # Convert a string true/false or 1/0 value to boolean.
   # @param [String] value The value to convert.
   # @return [true, false]
@@ -105,7 +117,108 @@ class OBAClient
     end
   end
 
-  # Parse the raw XML, returning a Hash with three elements: statistics,
+  # Attributes for mapping concepts (annotation concepts add one, 
+  # @see ANNOTATION_CONCEPT_ATTRIBUTES.
+  CONCEPT_ATTRIBUTES = {
+    :id              => lambda {|c| c.xpath("id").text.to_i},
+    :localConceptId  => lambda {|c| c.xpath("localConceptId").text},
+    :localOntologyId => lambda {|c| c.xpath("localOntologyId").text.to_i},
+    :isTopLevel      => lambda {|c| to_b(c.xpath("isTopLevel").text)},
+    :fullId          => lambda {|c| c.xpath("fullId").text},
+    :preferredName   => lambda {|c| c.xpath("preferredName").text},
+
+    :synonyms        => lambda do |c| 
+      c.xpath("synonyms/synonym").map do |s|
+        s.xpath("string").text
+      end
+    end,
+
+    :semanticTypes   => lambda do |c| 
+      c.xpath("semanticTypes/semanticTypeBean").map do |s|
+        {
+          :id           => s.xpath("id").text.to_i,
+          :semanticType => s.xpath("semanticType").text,
+          :description  => s.xpath("description").text
+        }
+      end
+    end
+  }
+  
+  # Annotation concepts have the same attributes as mapping concepts, plus one.
+  ANNOTATION_CONCEPT_ATTRIBUTES = CONCEPT_ATTRIBUTES.merge(
+    :mappingType => lambda {|c| c.xpath("mappingType").text}
+  )
+
+  #  # Toplevel attributes for annotation contexts.
+  ANNOTATION_CONTEXT_ATTRIBUTES = {
+    :score   => lambda {|c| c.xpath("score").text.to_i},
+    :concept => lambda {|c| parse_concept(c.xpath("concept").first)},
+    :context => lambda {|c| parse_context(c.xpath("context").first)}
+  }
+
+  # Toplevel attributes for all other contexts.
+  CONTEXT_ATTRIBUTES = {
+    :contextName     => lambda {|c| c.xpath("contextName").text},
+    :isDirect        => lambda {|c| to_b(c.xpath("isDirect").text)},
+    :from            => lambda {|c| c.xpath("from").text.to_i},
+    :to              => lambda {|c| c.xpath("to").text.to_i},
+  }
+
+  #  # Toplevel attributes for mapping contexts.
+  MAPPED_CONTEXT_ATTRIBUTES = CONTEXT_ATTRIBUTES.merge(
+    :mappedConcept => lambda {|c| parse_concept(c.xpath("mappedConcept").first)}
+  )
+
+  # Toplevel attributes for mgrep contexts.
+  MGREP_CONTEXT_ATTRIBUTES = CONTEXT_ATTRIBUTES.merge(
+    :name           => lambda {|c| c.xpath("term/name").text},
+    :localConceptId => lambda {|c| c.xpath("term/localConceptId").text},
+    :isPreferred    => lambda {|c| to_b(c.xpath("term/isPreferred").text)},
+    :dictionaryId   => lambda {|c| c.xpath("term/dictionaryId").text}
+  )
+
+  CONCEPT_TYPES = {
+    "concept"       => ANNOTATION_CONCEPT_ATTRIBUTES,
+    "mappedConcept" => CONCEPT_ATTRIBUTES
+  }
+
+  CONTEXT_CLASSES = {
+    "annotationContextBean"  => ANNOTATION_CONTEXT_ATTRIBUTES,
+    "mgrepContextBean"       => MGREP_CONTEXT_ATTRIBUTES,
+    "mappingContextBean"     => MAPPED_CONTEXT_ATTRIBUTES,
+  }
+
+  ##
+  # Parse a context - an annotation, or a mapping/mgrep context bean.
+  # @param [Nokgiri::XML::Node] context The root node of the context.
+  # @return Hash<Symbol, Object> The parsed context.
+  def self.parse_context(context)
+    # Annotations (annotationBeans) do not have a class, so we'll refer to them
+    # as annotationContextBeans
+    context_class = if context.attribute("class").nil?
+      "annotationContextBean"
+    else
+      context.attribute("class").value
+    end
+
+    Hash[CONTEXT_CLASSES[context_class].map do |k, v|
+      [k, v.call(context)]
+    end]
+  end
+
+  ##
+  # Parse a concept - a toplevel annotation concept, or an annotation's
+  # mapping concept.
+  # @param [Nokogiri::XML::Node] concept The root node of the concept.
+  # @return [Hash<Symbol, Object>] The parsed concept.
+  def self.parse_concept(concept)
+    Hash[CONCEPT_TYPES[concept.name].map do |k, v| 
+      [k, v.call(concept)]
+    end]
+  end
+
+  ##
+  # Parse raw XML, returning a Hash with three elements: statistics,
   # annotations, and ontologies. Respectively, these represent the annotation
   # statistics (annotations by mapping type, etc., as a Hash), an Array of
   # each annotation (as a Hash), and an Array of ontologies used (also as
@@ -114,46 +227,18 @@ class OBAClient
   # @return [Hash<Symbol, Object>] A Hash representation of the XML, as
   #   described above.
   def self.parse(xml)
-    statistics  = {}
-    annotations = []
-    ontologies  = []
     doc = Nokogiri::XML.parse(xml)
 
-    doc.xpath(STATISTICS_BEANS_XPATH).each do |sb|
-      statistics[sb.xpath("mapping").text] = sb.xpath("nbAnnotation").text.to_i
-    end
-  
-    doc.xpath(ANNOTATION_BEANS_XPATH).each do |ann|
-      parsed = {
-        :score           => ann.xpath("score").text.to_i,
-        :id              => ann.xpath("concept/id").text.to_i,
-        :localConceptId  => ann.xpath("concept/localConceptId").text,
-        :localOntologyId => ann.xpath("concept/localOntologyId").text.to_i,
-        :isTopLevel      => to_b(ann.xpath("concept/isTopLevel").text),
-        :fullId          => ann.xpath("concept/fullId").text,
-        :preferredName   => ann.xpath("concept/preferredName").text,
-        :mappingType     => ann.xpath("context/contextName").text,
-        :isDirect        => to_b(ann.xpath("context/isDirect").text)
-      }
+    statistics = Hash[doc.xpath(STATISTICS_BEANS_XPATH).map do |sb|
+      [sb.xpath("mapping").text, sb.xpath("nbAnnotation").text.to_i]
+    end]
 
-      synonyms = ann.xpath("concept/synonyms/synonym")
-      parsed[:synonyms] = synonyms.map do |synonym|
-        synonym.xpath("string").text
-      end
-
-      semanticTypeBeans = ann.xpath("concept/semanticTypes/semanticTypeBean")
-      parsed[:semanticTypes] = semanticTypeBeans.map do |semanticType|
-        {
-          :id           => semanticType.xpath("id").text.to_i,
-          :semanticType => semanticType.xpath("semanticType").text,
-          :description  => semanticType.xpath("description").text
-        }
-      end
-      annotations << parsed
+    annotations = doc.xpath(ANNOTATION_BEANS_XPATH).map do |annotation|
+      parse_context(annotation)
     end
 
-    doc.xpath(ONTOLOGY_BEANS_XPATH).each do |ontology|
-      ontologies << {
+    ontologies = doc.xpath(ONTOLOGY_BEANS_XPATH).map do |ontology|
+      {
         :localOntologyId   => ontology.xpath("localOntologyId").text.to_i,
         :virtualOntologyId => ontology.xpath("virtualOntologyId").text.to_i,
         :name              => ontology.xpath("name").text

data/test/test_oba_client.rb

@@ -1,12 +1,13 @@
 require "test/unit"
 require "oba_client"
+require "pp"
 
 TEST_TEXTS = [
-  "Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the thorax.",
-  %Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
-  aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
-  aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
-  }
+  "Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the thorax. large intestine thorax",
+#  %Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
+#  aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
+#  aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
+#  }
 ]
 
 class TestOBAClient < Test::Unit::TestCase
@@ -70,7 +71,22 @@ class TestOBAClient < Test::Unit::TestCase
     end
   end
   
+  def test_ontologies_pseudo_parameter
+    ann = OBAClient.new(:ontologies => [42812], :parse_xml => true)
+    TEST_TEXTS.each do |text|
+      parsed = ann.execute(text)
+      assert parsed[:ontologies].all? {|o| o[:localOntologyId] == 42812}
+    end
+  end
+  
   def test_parse
     parsed = OBAClient::parse("<?xml version='1.0'></xml>")
   end
+  
+  def test_with_print
+    ann = OBAClient.new(:ontologies => [42838, 35686], :parse_xml => false)
+    ann = OBAClient.new(:ontologies => [42838, 35686], :parse_xml => true)
+  end
+    
+  
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 15
   prerelease: false
   segments: 
-  - 1
   - 2
-  - 1
-  version: 1.2.1
+  - 0
+  - 0
+  version: 2.0.0
 platform: ruby
 authors: 
 - Rob Tirrell