bioportal 2.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 3b0961441bb3fba35541487be496d53e94520771
+  data.tar.gz: 2132cb61672cac93d978479222e120e952c48609
+SHA512:
+  metadata.gz: 2bc35cbc513e07023c8ed63fd46c79de75d1085be2a0a2d5f7b37327ae03a37dda01aca472e57d988bb1e1d01a136f0da0a20ee6ebe08ae1984cdf48b62f00a9
+  data.tar.gz: b46d595cfd2b4e125389da7616c6b69abd453eb40f23ef62e28be31f6abda1add61795e0d92594a113840f3e95ea0ddcb8efbe710ad1120f68fff1ed3c422781

data/.gitignore

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+*~
+test/bioportal_api_key
+.idea/

data/.ruby-gemset

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+bioportal-gem

data/BSD-LICENSE

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+Copyright (c) 2014, University of Manchester & HITS gGmbH
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice, this list of conditions
+      and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions
+      and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    * Neither the name of the University of Manchester or EML Research gGmbH,
+      nor the names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/Gemfile

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+source "https://rubygems.org"
+
+
+gem "rails","2.3.17",:group=>:test
+gem "test-unit",:group=>:test

data/Gemfile.lock

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+GEM
+  remote: https://rubygems.org/
+  specs:
+    actionmailer (2.3.17)
+      actionpack (= 2.3.17)
+    actionpack (2.3.17)
+      activesupport (= 2.3.17)
+      rack (~> 1.1.0)
+    activerecord (2.3.17)
+      activesupport (= 2.3.17)
+    activeresource (2.3.17)
+      activesupport (= 2.3.17)
+    activesupport (2.3.17)
+    rack (1.1.6)
+    rails (2.3.17)
+      actionmailer (= 2.3.17)
+      actionpack (= 2.3.17)
+      activerecord (= 2.3.17)
+      activeresource (= 2.3.17)
+      activesupport (= 2.3.17)
+      rake (>= 0.8.3)
+    rake (10.1.1)
+    test-unit (2.5.5)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  rails (= 2.3.17)
+  test-unit

data/README.rdoc

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+= Bioportal Gem
+
+A simple Gem for using the Bioportal API.
+
+This version was a cut-back implementation of a previous version that used the old BioPortal API. It was cut-back just to support
+the needs of the Seek for Science project - http://seek4science.org
+
+It supports simple searching and fetching details about a class in an ontology.
+
+
+

data/Rakefile

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+require 'rake'
+require 'rake/testtask'
+require 'rdoc/task'
+
+desc 'Default: run unit tests.'
+task :default => :test
+
+desc 'Test the bioportal plugin.'
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = true
+end
+
+desc 'Generate documentation for the bioportal plugin.'
+Rake::RDocTask.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'Bioportal Plugin'
+  rdoc.options << '--line-numbers' << '--inline-source'
+  rdoc.rdoc_files.include('README')
+  rdoc.rdoc_files.include('BSD-LICENSE')
+  rdoc.rdoc_files.include(['lib/**/*.rb','app/**/*.rb'])
+end

data/app/helpers/bio_portal_helper.rb

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+
+
+module BioPortalHelper
+
+  def visualise_ontology model,options={}
+    options[:show_concept]||=false
+    concept_id=nil
+    concept_id=model.concept_uri if options[:show_concept] && !model.concept_uri.nil?
+    ontology_id ||= model.ontology_id
+    apikey=options[:apikey]
+    render(:partial=>"bioportal/bioportal_visualise",:locals=>{:ontology_id=>ontology_id,:concept_id=>concept_id,:apikey=>apikey})
+  end
+
+
+
+end
+

data/app/models/bioportal_concept.rb

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+class BioportalConcept < ActiveRecord::Base
+  include BioPortal::RestAPI
+
+  belongs_to :conceptable,:polymorphic=>true
+
+  before_save :check_cached_concept
+
+  def get_concept options={}
+    options[:refresh]||=false
+    
+    refresh=options.delete(:refresh)
+    
+    concept=nil
+    concept = YAML::load(cached_concept_yaml) unless (refresh || cached_concept_yaml.nil?)
+    unless concept      
+      concept = super(self.ontology_id,self.concept_uri,options)
+      update_attribute(:cached_concept_yaml, concept.to_yaml)
+    end
+      
+    concept
+  end
+
+
+  #the base url is defined by the associated class - this overrides the method in the RestAPI mixin
+  def bioportal_base_rest_url
+    conceptable.bioportal_base_rest_url
+  end
+
+  protected
+
+  #invoked before_save, and if the ontology_id, ontology_version_id or concept_uri has changed then the cached concept will be cleared
+  def check_cached_concept
+    changed_fields = changes.keys
+    
+    if !(changed_fields & ["ontology_id","concept_uri"]).empty?
+      self.cached_concept_yaml=nil
+    end
+  end
+end

data/app/views/bioportal/_bioportal_visualise.html.erb

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+
+<iframe id="bioportal_visualisation" frameborder="0" src="http://bioportal.bioontology.org/widgets/visualization?ontology=<%=ontology_id%>&class=<%=URI.escape(concept_id,":/")%>&apikey=<%=apikey%>"></iframe>

data/bioportal.gemspec

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+Gem::Specification.new do |s|
+  s.name        = 'bioportal'
+  s.version     = '2.1'
+  s.date        = '2014-03-20'
+  s.summary     = "Supports linking of Models within a RoR application to a Concept and Ontology within the BioPortal"
+  s.authors     = ["Stuart Owen","Quyen Nguyen"]
+  s.email       = 'nttqa22001@yahoo.com'
+  s.files       = `git ls-files`.split("\n")
+  s.homepage    = 'https://github.com/SysMO-DB/bioportal'
+  s.require_paths = ["lib"]
+end

data/generators/bioportal_migration/USAGE

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+Description:
+    Explain the generator
+
+Example:
+    ./script/generate bioportal Thing
+
+    This will create:
+        what/will/it/create

data/generators/bioportal_migration/bioportal_migration_generator.rb

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+class BioportalMigrationGenerator < Rails::Generator::Base
+  def manifest
+    record do |m|
+      m.migration_template 'migration.rb', 'db/migrate', :migration_file_name => "bioportal_concept_migration"
+    end
+  end
+end

data/generators/bioportal_migration/templates/migration.rb

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+class BioportalConceptMigration < ActiveRecord::Migration
+  def self.up
+    create_table :bioportal_concepts do |t|
+      t.column :ontology_id, :integer
+      t.column :ontology_version_id,:integer
+      t.column :concept_uri,:string
+      t.column :cached_concept_yaml,:text
+      t.column :conceptable_id,:integer
+      t.column :conceptable_type,:string
+    end        
+  end
+  
+  def self.down
+    drop_table :bioportal_concepts
+  end
+end

data/install.rb

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+# Install hook code here

data/lib/bioportal.rb

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+require 'pp'
+module BioPortal
+  
+  require 'bioportal/engine' if defined?(Rails)
+  
+  module Acts
+    def self.included(mod)
+      mod.extend(ClassMethods)
+    end
+
+    module ClassMethods
+      def linked_to_bioportal(options = {}, &extension)
+        options[:base_url]||="http://data.bioontology.org"
+        
+        has_one :bioportal_concept,:as=>:conceptable,:dependent=>:destroy
+        before_save :save_changed_concept
+        cattr_accessor :bioportal_base_rest_url, :bioportal_api_key
+
+        self.bioportal_base_rest_url=options[:base_url]
+        self.bioportal_api_key=options[:apikey]
+
+
+        extend BioPortal::Acts::SingletonMethods
+        include BioPortal::Acts::InstanceMethods        
+      end
+    end
+
+    module SingletonMethods
+      
+    end
+
+    module InstanceMethods
+     
+      def concept options={}
+
+        options[:apikey] ||= self.bioportal_api_key unless self.bioportal_api_key.nil?
+
+        return nil if self.bioportal_concept.nil?
+        begin
+          return self.bioportal_concept.get_concept options
+        rescue Exception=>e
+          return nil
+        end
+      end
+
+      def ncbi_uri
+        concept_uri
+      end
+
+      def ncbi_id
+        unless ncbi_uri.nil?
+          id = ncbi_uri.split("/").last.split("_").last
+          id.to_i
+        else
+          nil
+        end
+      end
+
+
+      def ontology_id
+        return nil if self.bioportal_concept.nil?
+        return self.bioportal_concept.ontology_id
+      end
+
+
+      def concept_uri
+        return nil if self.bioportal_concept.nil?
+        return self.bioportal_concept.concept_uri
+      end
+
+      def ontology_id= value
+        check_concept
+        self.bioportal_concept.ontology_id=value
+      end
+
+
+      def concept_uri= value
+        check_concept
+        self.bioportal_concept.concept_uri=value
+      end   
+
+      private
+
+      def check_concept
+        self.bioportal_concept=BioportalConcept.new if self.bioportal_concept.nil?
+      end
+
+      def save_changed_concept
+        self.bioportal_concept.save! if !self.bioportal_concept.nil? && self.bioportal_concept.changed?
+      end
+
+    end
+  end
+  
+
+  module RestAPI
+    require 'rubygems'
+    require 'open-uri'
+    require 'uri'
+
+    
+    
+    def get_concept ontology_acronym,class_id,options={}
+      url = "/ontologies/#{ontology_acronym}/classes/#{URI.escape(class_id,":/")}?"
+      options.keys.each{|key| url += "#{key.to_s}=#{URI.encode(options[key].to_s)}&"}
+      url=bioportal_base_rest_url+url
+      json = fetch_json(url)
+      concept={}
+      concept[:label]=json["prefLabel"]
+      concept[:synonyms]=json["synonym"]
+      concept[:definitions]=json["definition"]
+      concept
+    end
+
+
+    def search query,options={}
+      options[:pagesize] ||= 10
+      options[:page] ||= 1
+      
+      search_url="/search?q=%QUERY%&"
+      options.keys.each {|key| search_url+="#{key.to_s}=#{URI.encode(options[key].to_s)}&"}
+      search_url=search_url[0..-2] #chop of trailing &
+      
+      search_url=search_url.gsub("%QUERY%",URI.encode(query))
+      full_search_path=bioportal_base_rest_url+search_url
+
+      json = fetch_json(full_search_path)
+
+      results = json["collection"].collect do |item|
+        res = {}
+        res[:ontology_link]=item["links"]["ontology"]
+        res[:class_link]=item["links"]["self"]
+        res[:preferred_label]=item["prefLabel"]
+        res[:synonyms]=item["synonym"] || []
+        res[:class_id]=item["@id"]
+        populate_ontology_details res,options
+        res
+      end
+      pages = json["pageCount"]
+
+      return results.uniq,pages.to_i
+    end
+
+    def populate_ontology_details search_result, options
+      apikey = options[:apikey]
+      link = search_result[:ontology_link]
+      link = link+"?apikey=#{apikey}"
+      json = fetch_json(link)
+
+      search_result[:ontology_name]=json["name"]
+      search_result[:ontology_acronym]=json["acronym"]
+    end
+
+    def fetch_json link
+      @@bioportal_json ||={}
+      json = @@bioportal_json[link]
+      if json.nil?
+        json = JSON.parse(open(link).read)
+        @@bioportal_json[link]=json
+      end
+      json
+    end
+
+
+    private
+    
+    DEFAULT_REST_URL = "http://data.bioontology.org"
+
+    def bioportal_base_rest_url
+      DEFAULT_REST_URL
+    end
+
+  end
+    
+end
+
+ActiveRecord::Base.send(:include,BioPortal::Acts)
+

data/lib/bioportal/engine.rb

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+module BioPortal
+  class Engine < ::Rails::Engine
+
+  end
+end

data/lib/tasks/bioportal_tasks.rake

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+# desc "Explaining what the task does"
+# task :bioportal do
+#   # Task goes here
+# end

data/rdoc/classes/BioPortal.html

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+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Module: BioPortal</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+
+    elemStyle = elem.style;
+    
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+
+    return true;
+  }
+  
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  
+  // ]]>
+  </script>
+
+</head>
+<body>
+
+
+
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Module</strong></td>
+          <td class="class-name-in-header">BioPortal</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/lib/bioportal_rb.html">
+                lib/bioportal.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+
+        </table>
+    </div>
+  <!-- banner header -->
+
+  <div id="bodyContent">
+
+
+
+  <div id="contextContent">
+
+
+
+   </div>
+
+
+  </div>
+
+
+    <!-- if includes -->
+
+    <div id="section">
+
+    <div id="class-list">
+      <h3 class="section-bar">Classes and Modules</h3>
+
+      Module <a href="BioPortal/Acts.html" class="link">BioPortal::Acts</a><br />
+Module <a href="BioPortal/RestAPI.html" class="link">BioPortal::RestAPI</a><br />
+
+    </div>
+
+
+
+
+      
+
+
+    <!-- if method_list -->
+
+
+  </div>
+
+
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+
+</body>
+</html>