drugbank 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in drugbank.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Eric Harrison
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Drugbank
+
+Simple Gem (for now) that allows you to import the drugbank.ca xml
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'drugbank'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install drugbank
+
+## Usage
+
+importer = Drugbank::Import.new('http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip')
+importer.import(){|drugs|  #do something }
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/drugbank.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'drugbank/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "drugbank"
+  gem.version       = Drugbank::VERSION
+  gem.authors       = ["Eric Harrison"]
+  gem.email         = ["eharrison@smashtankapps.com"]
+  gem.description   = %q{Download the xml from Drugbank.ca and import}
+  gem.summary       = %q{Importer for Drugbank.ca}
+  gem.homepage      = "http://github.com/smashtank/drugbank"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency "sax_stream", "1.0.3"
+  gem.add_dependency "rubyzip", "0.9.9"
+end

data/lib/drugbank.rb

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+require "drugbank/version"
+
+require 'net/http'
+
+require 'sax_stream/mapper'
+require 'sax_stream/parser'
+
+Dir["#{File.dirname(__FILE__)}/drugbank/*.rb"].each { |f| require(f) }
+
+module Drugbank
+end

data/lib/drugbank/atc_code.rb

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+require 'drugbank/base'
+
+module Drugbank
+  class AtcCode < Drugbank::Base
+    include SaxStream::Mapper
+    node 'atc-code'
+    map :code, :to => ''
+  end
+end

data/lib/drugbank/base.rb

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+module Drugbank
+  class Base
+    def method_missing(method, *args, &block)
+      if self.attributes.keys.include?(method.to_s)
+        self.class.send(:define_method, method,lambda{ self[method.to_s]})
+        return self[method.to_s]
+      elsif self.relations.keys.include?(method.to_s)
+        self.class.send(:define_method, method,lambda{ self.relations[method.to_s]})
+        return self.relations[method.to_s]
+      else
+        super
+      end
+    end
+  end
+end

data/lib/drugbank/brand.rb

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+require 'drugbank/base'
+module Drugbank
+  class Brand < Drugbank::Base
+    include SaxStream::Mapper
+    node 'brand'
+    map :name, :to => ''
+  end
+end

data/lib/drugbank/category.rb

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+require 'drugbank/base'
+module Drugbank
+  class Category < Drugbank::Base
+    include SaxStream::Mapper
+    node 'category'
+    map :name, :to => ''
+  end
+end

data/lib/drugbank/collector.rb

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+module Drugbank
+  class Collector
+    def initialize(batch_size, &block)
+      @batch_size = batch_size
+      @counter = 0
+      @batch = []
+      self.block = block
+    end
+
+    def <<(value)
+      @batch << value
+      @counter += 1
+      collect_batch if @counter % @batch_size == 0
+    end
+
+    def collect_batch
+      process_batch unless @batch.empty?
+      @batch = []
+      puts "  #{@counter}"
+    end
+
+    def block=(block)
+      @block = block
+    end
+
+    def process_batch
+      puts "Processing batch .."
+      errors = []
+      begin
+        block.call(@batch, errors)
+      rescue Exception => e
+        errors << "Error: BATCH FAILED - #{e.message}"
+      ensure
+        puts errors.join("\n")
+        puts "..done"
+      end
+    end
+
+    private
+    def block
+      @block
+    end
+  end
+end

data/lib/drugbank/dosage.rb

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+require 'drugbank/base'
+module Drugbank
+  class Dosage < Drugbank::Base
+    include SaxStream::Mapper
+
+    node 'dosage'
+
+    map :form,     :to => 'form'
+    map :route,    :to => 'route'
+    map :strength, :to => 'strength'
+  end
+end

data/lib/drugbank/drug.rb

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+require 'drugbank/base'
+require 'drugbank/secondary_accession_number'
+require 'drugbank/group'
+require 'drugbank/brand'
+require 'drugbank/synonym'
+require 'drugbank/packager'
+require 'drugbank/manufacturer'
+require 'drugbank/price'
+require 'drugbank/category'
+require 'drugbank/dosage'
+require 'drugbank/atc_code'
+require 'drugbank/patent'
+require 'drugbank/drug_interaction'
+require 'drugbank/external_id'
+require 'drugbank/external_link'
+
+module Drugbank
+  class Drug < Drugbank::Base
+    include SaxStream::Mapper
+
+    node 'drug'
+    map :id,                     :to => 'drugbank-id'
+    map :type,                   :to => '@type'
+    map :name,                   :to => 'name'
+    map :description,            :to => 'description'
+    map :cas_registry_number,    :to => 'cas-number'
+    map :general_references,     :to => 'general-references'
+    map :synthesis_references,   :to => 'synthesis-references'
+    map :indication,             :to => 'indication'
+    map :pharmacology,           :to => 'pharmacology'
+    map :mechanism_of_action,    :to => 'mechanism-of-action'
+    map :toxicity,               :to => 'toxicity'
+    map :biotransformation,      :to => 'biotransformation'
+    map :absorption,             :to => 'absorption'
+    map :half_life,              :to => 'half-life'
+    map :protein_binding,        :to => 'protein-binding'
+    map :route_of_elimination,   :to => 'route-of-elimination'
+    map :volume_of_distribution, :to => 'volume-of-distribution'
+    map :clearance,              :to => 'clearance'
+
+    relate :secondary_accession_numbers, :to => 'secondary-accession-numbers/secondary_accession_number', :as => [Drugbank::SecondaryAccessionNumber], :parent_collects => true
+    relate :brands,             :to => 'brands/brand',                              :as => [Drugbank::Brand],           :parent_collects => true
+    relate :groups,             :to => 'groups/group',                              :as => [Drugbank::Group],           :parent_collects => true
+    relate :synonyms,           :to => 'synonyms/synonym',                          :as => [Drugbank::Synonym],         :parent_collects => true
+    relate :packagers,          :to => 'packagers/packager',                        :as => [Drugbank::Packager],        :parent_collects => true
+    relate :manufacturers,      :to => 'manufacturers/manufacturer',                :as => [Drugbank::Manufacturer],    :parent_collects => true
+    relate :prices,             :to => 'prices/price',                              :as => [Drugbank::Price],           :parent_collects => true
+    relate :categories,         :to => 'categories/category',                       :as => [Drugbank::Category],        :parent_collects => true
+    relate :dosages,            :to => 'dosages/dosage',                            :as => [Drugbank::Dosage],          :parent_collects => true
+    relate :atc_codes,          :to => 'atc-codes/atc-code',                        :as => [Drugbank::AtcCode],         :parent_collects => true
+    relate :patents,            :to => 'patents/patent',                            :as => [Drugbank::Patent],          :parent_collects => true
+    relate :drug_interactions,  :to => 'drug-interactions/drug-interaction',        :as => [Drugbank::DrugInteraction], :parent_collects => true
+    relate :external_ids,       :to => 'external-identifiers/external-identifier',  :as => [Drugbank::ExternalId],      :parent_collects => true
+    relate :external_links,     :to => 'external-links/external-link',              :as => [Drugbank::ExternalLink],    :parent_collects => true
+    
+  end
+end

data/lib/drugbank/drug_interaction.rb

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+require 'drugbank/base'
+module Drugbank
+  class DrugInteraction < Drugbank::Base
+    include SaxStream::Mapper
+
+    node 'drug-interaction'
+    map :interaction_drug_id, :to => 'drug'
+    map :name,                :to => 'name'
+    map :description,         :to => 'description'
+  end
+end

data/lib/drugbank/drugs.rb

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+require 'drugbank/base'
+require 'drugbank/drug'
+
+module Drugbank
+  class Drugs < Drugbank::Base
+    include SaxStream::Mapper
+    node 'drugs', :collect => false
+
+    relate :drugs, :to => 'drug',  :as => [Drugbank::Drug]
+  end
+end
+

data/lib/drugbank/external_id.rb

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+require 'drugbank/base'
+module Drugbank
+  class ExternalId < Drugbank::Base
+    include SaxStream::Mapper
+
+    map :resource,  :to => 'resource'
+    map :id,        :to => 'identifier'
+  end
+end

data/lib/drugbank/external_link.rb

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+require 'drugbank/base'
+module Drugbank
+  class ExternalLink < Drugbank::Base
+    include SaxStream::Mapper
+    map :resource,  :to => 'resource'
+    map :url,        :to => 'url'
+  end
+end

data/lib/drugbank/group.rb

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+require 'drugbank/base'
+module Drugbank
+  class Group < Drugbank::Base
+    include SaxStream::Mapper
+
+    map :name, :to => ''
+  end
+end

data/lib/drugbank/import.rb

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+require 'zip/zip'
+require 'net/http'
+require 'open-uri' #incase we can
+require 'uri'
+require 'tempfile'
+require 'digest/md5'
+require 'zip/zip'
+
+require 'drugbank/drugs'
+require 'drugbank/collector'
+
+module Drugbank
+  class Import
+    include ObjectSpace
+
+    def initialize(url, batch_size = 500)
+      @batch_size = batch_size
+      @url = url
+    end
+
+    def parser
+      @parser ||= SaxStream::Parser.new(collector, [Drugbank::Drugs])
+    end
+
+    def collector
+      @collector ||= Drugbank::Collector.new(@batch_size)
+    end
+
+    def import(&block)
+      set_collector_block(block)
+      parser.parse_stream(fetch_url(@url))
+      collector.collect_batch
+    end
+
+    private 
+      def set_collector_block(block)
+        collector.block = block
+      end
+
+      def add_file_for_cleanup(file)
+        define_finalizer(self, lambda{|id| file.respond_to?(:unlink) ? file.unlink : File.unlink(file) })
+      end
+
+      def file_name
+        "drugbank_import-#{Digest::MD5.hexdigest(@url)}.zip"
+      end
+
+      def fetch_url(url)
+        case url.split(/\./).last
+        when 'zip'
+          zip_file = open(file_name, 'wb')
+          add_file_for_cleanup(file_name)
+          begin
+            uri = URI.parse(url)
+            Net::HTTP.start(uri.host, uri.port) do |http|
+              http.request_get(uri.request_uri) do |resp|
+                  resp.read_body do |segment|
+                      zip_file.write(segment)
+                  end
+              end
+            end
+          ensure
+            zip_file.close()
+          end
+          #unzip the file first
+          Zip::ZipInputStream::open(file_name) do |io|    
+            while (entry = io.get_next_entry)
+              if entry.name.split(/\./).last == 'xml'
+                unziped_file = Tempfile.new(Digest::MD5.hexdigest(entry.name))
+                add_file_for_cleanup(unziped_file)
+                unziped_file.write(io.read)
+                unziped_file.close()
+                return open(unziped_file.path)
+              end
+            end
+          end
+        else
+          return open(url)
+        end
+    end
+  end
+end

data/lib/drugbank/manufacturer.rb

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+require 'drugbank/base'
+module Drugbank
+  class Manufacturer < Drugbank::Base
+    include SaxStream::Mapper
+
+    map :generic, :to => '@generic'
+    map :name,    :to => ''
+  end
+end

data/lib/drugbank/packager.rb

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+require 'drugbank/base'
+module Drugbank
+  class Packager < Drugbank::Base
+    include SaxStream::Mapper
+    map :name,  :to => 'name'
+    map :url,        :to => 'url'
+  end
+end

data/lib/drugbank/patent.rb

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+require 'drugbank/base'
+module Drugbank
+  class Patent < Drugbank::Base
+    include SaxStream::Mapper
+
+    map :number,      :to => 'number'
+    map :country,     :to => 'country'
+    map :expires_at,  :to => 'expires'
+    map :approved_at, :to => 'approved'
+  end
+end

data/lib/drugbank/price.rb

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+require 'drugbank/base'
+module Drugbank
+  class Price < Drugbank::Base
+    include SaxStream::Mapper
+    map :description, :to => 'description'
+    map :cost, :to => 'cost'
+    map :currency, :to => 'cost@currency'
+    map :unit, :to => 'unit'
+  end
+end

data/lib/drugbank/secondary_accession_number.rb

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+require 'drugbank/base'
+module Drugbank
+  class SecondaryAccessionNumber < Drugbank::Base
+    include SaxStream::Mapper
+    node 'secondary-accession-number'
+
+    map :number, :to => ''
+  end
+end

data/lib/drugbank/synonym.rb

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+require 'drugbank/base'
+module Drugbank
+  class Synonym < Drugbank::Base
+    include SaxStream::Mapper
+
+    node 'synonym'
+    map :name, :to => ''
+  end
+end

data/lib/drugbank/version.rb

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+module Drugbank
+  VERSION = "0.0.1"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: drugbank
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Eric Harrison
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-08-05 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: sax_stream
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.3
+- !ruby/object:Gem::Dependency
+  name: rubyzip
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+description: Download the xml from Drugbank.ca and import
+email:
+- eharrison@smashtankapps.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- drugbank.gemspec
+- lib/.DS_Store
+- lib/drugbank.rb
+- lib/drugbank/.DS_Store
+- lib/drugbank/atc_code.rb
+- lib/drugbank/base.rb
+- lib/drugbank/brand.rb
+- lib/drugbank/category.rb
+- lib/drugbank/collector.rb
+- lib/drugbank/dosage.rb
+- lib/drugbank/drug.rb
+- lib/drugbank/drug_interaction.rb
+- lib/drugbank/drugs.rb
+- lib/drugbank/external_id.rb
+- lib/drugbank/external_link.rb
+- lib/drugbank/group.rb
+- lib/drugbank/import.rb
+- lib/drugbank/manufacturer.rb
+- lib/drugbank/packager.rb
+- lib/drugbank/patent.rb
+- lib/drugbank/price.rb
+- lib/drugbank/secondary_accession_number.rb
+- lib/drugbank/synonym.rb
+- lib/drugbank/version.rb
+homepage: http://github.com/smashtank/drugbank
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Importer for Drugbank.ca
+test_files: []