bioportal 2.1

data/test/bioportal_test.rb

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+require_relative 'test_helper'
+require 'pp'
+
+
+class BioportalTest < Test::Unit::TestCase
+  
+  include BioPortal::RestAPI
+
+  def setup
+    @options={:apikey=>read_bioportal_api_key}
+  end
+  
+  def test_search
+    @options[:pagesize]=10
+    res,pages = search "Escherichia coli",@options
+
+    assert !res.empty?
+    assert pages>50
+    assert_equal 10,res.size
+
+    found = res.find{|r| r[:class_id]=="http://purl.bioontology.org/ontology/MSH/D004926"}
+    assert_not_nil(found)
+    assert_equal "http://data.bioontology.org/ontologies/MESH",found[:ontology_link]
+    assert_equal "Medical Subject Headings",found[:ontology_name]
+    assert_equal "MESH",found[:ontology_acronym]
+
+  end
+
+  def test_search_specific_ontologies
+    @options[:pagesize]=150
+    @options[:ontologies]="NCBITAXON"
+    res,pages = search "cat",@options
+
+    assert !res.empty?
+    assert res.size>50
+    assert_equal 1,pages
+
+    assert_empty(res.select{|r| r[:ontology_link]!="http://data.bioontology.org/ontologies/NCBITAXON"})
+  end
+
+  def test_get_concept
+    concept = get_concept "NCBITAXON","http://purl.obolibrary.org/obo/NCBITaxon_431941",@options
+    assert_not_nil concept, "concept returned should not be nil"
+    assert_equal "Rana megatympanum",concept[:label]
+
+    assert concept[:synonyms].include?("tobacco frog"),"synonyms should contain tobacco frog"
+    assert_equal [], concept[:definitions]
+  end
+
+  def test_override_base_url
+    class << self
+      def bioportal_base_rest_url
+        "http://google.com/fred"
+      end
+    end
+    assert_raise(OpenURI::HTTPError) { get_concept "NCBITAXON","http://purl.obolibrary.org/obo/NCBITaxon_431941",{:light=>true}  }
+  end
+
+  
+end

data/test/test_helper.rb

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+require 'rubygems'
+require 'active_support'
+require 'active_support/test_case'
+require 'active_record'
+require_relative '../lib/bioportal'
+
+class Test::Unit::TestCase
+  def read_bioportal_api_key
+    path = File.join(File.dirname(__FILE__),"bioportal_api_key")
+
+    if File.exist?(path)
+      @@bioportal_api_key ||= File.new(path).read
+      @@bioportal_api_key
+    else
+      raise "You need a file test/bioportal_api_key which contains a string containing your api key. Without this, tests cannot run"
+    end
+  end
+end

data/uninstall.rb

@@ -0,0 +1 @@
+# Uninstall hook code here

metadata

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+--- !ruby/object:Gem::Specification
+name: bioportal
+version: !ruby/object:Gem::Version
+  version: '2.1'
+platform: ruby
+authors:
+- Stuart Owen
+- Quyen Nguyen
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-03-20 00:00:00.000000000 Z
+dependencies: []
+description: 
+email: nttqa22001@yahoo.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".ruby-gemset"
+- BSD-LICENSE
+- Gemfile
+- Gemfile.lock
+- README.rdoc
+- Rakefile
+- app/helpers/bio_portal_helper.rb
+- app/models/bioportal_concept.rb
+- app/views/bioportal/_bioportal_visualise.html.erb
+- bioportal.gemspec
+- generators/bioportal_migration/USAGE
+- generators/bioportal_migration/bioportal_migration_generator.rb
+- generators/bioportal_migration/templates/migration.rb
+- install.rb
+- lib/bioportal.rb
+- lib/bioportal/engine.rb
+- lib/tasks/bioportal_tasks.rake
+- rdoc/classes/BioPortal.html
+- rdoc/classes/BioPortal/Acts.html
+- rdoc/classes/BioPortal/Acts/ClassMethods.html
+- rdoc/classes/BioPortal/Acts/InstanceMethods.html
+- rdoc/classes/BioPortal/Acts/SingletonMethods.html
+- rdoc/classes/BioPortal/RestAPI.html
+- rdoc/classes/BioPortalHelper.html
+- rdoc/classes/BioportalConcept.html
+- rdoc/created.rid
+- rdoc/files/BSD-LICENSE.html
+- rdoc/files/README.html
+- rdoc/files/app/helpers/bio_portal_helper_rb.html
+- rdoc/files/app/models/bioportal_concept_rb.html
+- rdoc/files/lib/bioportal_rb.html
+- rdoc/fr_class_index.html
+- rdoc/fr_file_index.html
+- rdoc/fr_method_index.html
+- rdoc/index.html
+- rdoc/rdoc-style.css
+- test/bioportal_test.rb
+- test/test_helper.rb
+- uninstall.rb
+homepage: https://github.com/SysMO-DB/bioportal
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Supports linking of Models within a RoR application to a Concept and Ontology
+  within the BioPortal
+test_files: []