oddb2xml 1.1.2 → 1.1.3

data/Gemfile

@@ -1,14 +1,3 @@
 source :rubygems
 
-gem 'rubyzip'
-gem 'archive-tar-minitar'
-gem 'mechanize'
-gem 'nokogiri'
-gem 'savon', '>= 2.0'
-gem 'spreadsheet'
-
-group :development do
-  gem 'rspec'
-  gem 'webmock'
-  gem 'ZenTest'
-end
+gemspec

data/History.txt

@@ -1,3 +1,11 @@
+=== 1.1.3 / 09.01.2013
+
+* Add interaction.xml and code.xml output
+* Update to check option fi
+* Improve using of memory at file reading for mswin
+* Add oddb_fi_product.xml output to fi option
+* Restore Gemfile to use gemspec file
+
 === 1.1.2 / 08.01.2013
 
 * Update Gemfile for development

data/Manifest.txt

@@ -14,11 +14,15 @@ lib/oddb2xml/compressor.rb
 lib/oddb2xml/downloader.rb
 lib/oddb2xml/extractor.rb
 lib/oddb2xml/version.rb
+oddb2xml.gemspec
 spec/builder_spec.rb
 spec/cli_spec.rb
 spec/compressor_spec.rb
 spec/data/XMLPublications.zip
+spec/data/epha_interactions.csv
 spec/data/oddb_article.xml
+spec/data/oddb_fi.xml
+spec/data/oddb_fi_product.xml
 spec/data/oddb_limitation.xml
 spec/data/oddb_product.xml
 spec/data/oddb_substance.xml
@@ -29,6 +33,7 @@ spec/data/swissmedic_fridges.html
 spec/data/swissmedic_fridges.xls
 spec/data/swissmedic_info.html
 spec/data/swissmedic_info.zip
+spec/data/swissmedic_info_2.html
 spec/data/swissmedic_orphans.html
 spec/data/swissmedic_orphans.xls
 spec/data/wsdl.xml

data/lib/oddb2xml/builder.rb

@@ -17,14 +17,17 @@ end
 
 module Oddb2xml
   class Builder
-    attr_accessor :subject, :index, :items, :infos,
+    attr_accessor :subject, :index, :items,
+                  :actions,
                   :orphans, :fridges,
+                  :infos,
                   :tag_suffix
     def initialize
       @subject    = nil
       @index      = {}
       @items      = {}
       @infos      = {}
+      @actions    = []
       @orphans    = []
       @fridges    = []
       @tag_suffix = nil
@@ -40,6 +43,21 @@ module Oddb2xml
       end
     end
     private
+    def prepare_articles
+      unless @articles
+        @articles = [] # base is 'DE'
+        @index['DE'].each_pair do |pharmacode, index|
+          object = {
+            :de => index,
+            :fr => @index['FR'][pharmacode],
+          }
+          if seq = @items[pharmacode]
+            object[:seq] = seq
+          end
+          @articles << object
+        end
+      end
+    end
     def prepare_substances
       unless @substances
         @substances = []
@@ -64,6 +82,45 @@ module Oddb2xml
         @limitations.sort_by!{|lim| lim[:code] }
       end
     end
+    def prepare_interactions
+      unless @interactions
+        @interactions = []
+        @actions.each do |act|
+          @interactions << act
+        end
+      end
+    end
+    def prepare_codes
+      unless @codes
+        @codes = {
+          'X' => {:int => 11, :txt => 'Kontraindiziert'},
+          'E' => {:int => 12, :txt => 'Kontraindiziert'},
+          'D' => {:int => 13, :txt => 'Kombination meiden'},
+          'C' => {:int => 14, :txt => 'Monitorisieren'},
+          'B' => {:int => 15, :txt => 'Vorsichtsmassnahmen'},
+          'A' => {:int => 16, :txt => 'keine Massnahmen'}
+        }
+      end
+    end
+    def prepare_products
+      unless @products
+        # merge company info from swissINDEX
+        @products = []
+        @products = @items.values.uniq.map do |seq|
+          %w[de fr].each do |lang|
+            name_key = "company_name_#{lang}".intern
+            seq[name_key] = ''
+            if pharmacode = seq[:pharmacodes].first
+              indices = @index[lang.upcase]
+              if index = indices[pharmacode]
+                seq[name_key] = index[:company_name]
+              end
+            end
+          end
+          seq
+        end
+      end
+    end
     def build_substance
       prepare_substances
       _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
@@ -133,23 +190,109 @@ module Oddb2xml
       end
       _builder.to_xml
     end
-    def build_product
-      prepare_substances
-      # merge company info from swissINDEX
-      objects = []
-      objects = @items.values.uniq.map do |seq|
-        %w[de fr].each do |lang|
-          name_key = "company_name_#{lang}".intern
-          seq[name_key] = ''
-          if pharmacode = seq[:pharmacodes].first
-            indices = @index[lang.upcase]
-            if index = indices[pharmacode]
-              seq[name_key] = index[:company_name]
-            end
+    def build_interaction
+      prepare_interactions
+      prepare_codes
+      _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
+        xml.doc.tag_suffix = @tag_suffix
+        datetime = Time.new.strftime('%FT%T.%7N%z')
+        xml.INTERACTION(
+          'xmlns:xsd'         => 'http://www.w3.org/2001/XMLSchema',
+          'xmlns:xsi'         => 'http://www.w3.org/2001/XMLSchema-instance',
+          'xmlns'             => 'http://wiki.oddb.org/wiki.php?pagename=Swissmedic.Datendeklaration',
+          'CREATION_DATETIME' => datetime,
+          'PROD_DATE'         => datetime,
+          'VALID_DATE'        => datetime,
+        ) {
+          @interactions.sort_by{|ix| ix[:ixno] }.each do |ix|
+            xml.IX('DT' => '') {
+              xml.IXNO ix[:ixno]
+              #xml.TITD
+              #xml.TITF
+              xml.GRP1D ix[:atc1]
+              #xml.GRP1F
+              xml.GRP2D ix[:atc2]
+              #xml.GRP2F
+              xml.EFFD  ix[:effect]
+              #xml.EFFF
+              if dict = @codes[ix[:grad].upcase]
+                xml.RLV  dict[:int]
+                xml.RLVD dict[:txt]
+                #xml.RLVF
+              end
+              #xml.EFFTXTD
+              #xml.EFFTXTF
+              xml.MECHD ix[:mechanism]
+              #xml.MECHF
+              xml.MEASD ix[:measures]
+              #xml.MEASF
+              #xml.REMD
+              #xml.REMF
+              #xml.LIT
+              xml.DEL false
+              #xml.IXMCH {
+              #  xml.TYP
+              #  xml.TYPD
+              #  xml.TYPF
+              #  xml.CD
+              #  xml.CDD
+              #  xml.CDF
+              #  xml.TXTD
+              #  xml.TXTF
+              #}
+            }
           end
-        end
-        seq
+          xml.RESULT {
+            xml.OK_ERROR   'OK'
+            xml.NBR_RECORD @interactions.length.to_s
+            xml.ERROR_CODE ''
+            xml.MESSAGE    ''
+          }
+        }
       end
+      _builder.to_xml
+    end
+    def build_code
+      prepare_codes
+      _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
+        xml.doc.tag_suffix = @tag_suffix
+        datetime = Time.new.strftime('%FT%T.%7N%z')
+        xml.CODE(
+          'xmlns:xsd'         => 'http://www.w3.org/2001/XMLSchema',
+          'xmlns:xsi'         => 'http://www.w3.org/2001/XMLSchema-instance',
+          'xmlns'             => 'http://wiki.oddb.org/wiki.php?pagename=Swissmedic.Datendeklaration',
+          'CREATION_DATETIME' => datetime,
+          'PROD_DATE'         => datetime,
+          'VALID_DATE'        => datetime,
+        ) {
+          @codes.each_pair do |val, definition|
+            xml.CD('DT' => '') {
+              xml.CDTYP   definition[:int]
+              xml.CDVAL   val
+              xml.DSCRSD  definition[:txt]
+              #xml.DSCRSF
+              #xml.DSCRMD
+              #xml.DSCRMF
+              #xml.DSCRD
+              #xml.DSCRF
+              xml.DEL false
+            }
+          end
+          xml.RESULT {
+            xml.OK_ERROR   'OK'
+            xml.NBR_RECORD @codes.keys.length
+            xml.ERROR_CODE ''
+            xml.MESSAGE    ''
+          }
+        }
+      end
+      _builder.to_xml
+    end
+    def build_product
+      prepare_substances
+      prepare_products
+      prepare_interactions
+      prepare_codes
       _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
         xml.doc.tag_suffix = @tag_suffix
         datetime = Time.new.strftime('%FT%T.%7N%z')
@@ -161,7 +304,7 @@ module Oddb2xml
           'PROD_DATE'         => datetime,
           'VALID_DATE'        => datetime,
         ) {
-          objects.each do |seq|
+          @products.each do |seq|
             xml.PRD('DT' => '') {
               xml.PRDNO seq[:product_key] unless seq[:product_key].empty?
               %w[de fr].each do |l|
@@ -245,11 +388,15 @@ module Oddb2xml
                     #xml.WHK
                   }
                 end
-                #xml.CPTIX {
-                  #xml.IXNO
-                  #xml.GRP
-                  #xml.RLV
-                #}
+                @interactions.each do |ix|
+                  if [ix[:act1], ix[:act2]].include?(seq[:atc_code])
+                    xml.CPTIX {
+                      xml.IXNO ix[:ixno]
+                      #xml.GRP
+                      xml.RLV  @codes[ix[:grad]]
+                    }
+                  end
+                end
                 #xml.CPTROA {
                   #xml.SYSLOC
                   #xml.ROA
@@ -266,7 +413,7 @@ module Oddb2xml
           end
           xml.RESULT {
             xml.OK_ERROR   'OK'
-            xml.NBR_RECORD objects.length.to_s
+            xml.NBR_RECORD @products.length.to_s
             xml.ERROR_CODE ''
             xml.MESSAGE    ''
           }
@@ -276,17 +423,7 @@ module Oddb2xml
     end
     def build_article
       prepare_limitations
-      objects = [] # base is 'DE'
-      @index['DE'].each_pair do |pharmacode, index|
-        object = {
-          :de => index,
-          :fr => @index['FR'][pharmacode],
-        }
-        if seq = @items[pharmacode]
-          object[:seq] = seq
-        end
-        objects << object
-      end
+      prepare_articles
       _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
         xml.doc.tag_suffix = @tag_suffix
         datetime = Time.new.strftime('%FT%T.%7N%z')
@@ -298,7 +435,7 @@ module Oddb2xml
           'PROD_DATE'         => datetime,
           'VALID_DATE'        => datetime,
         ) {
-          objects.each do |obj|
+          @articles.each do |obj|
             de_pac = obj[:de] # swiss index DE (base)
             fr_pac = obj[:fr] # swiss index FR
             bg_pac = nil      # BAG XML (additional data)
@@ -440,7 +577,7 @@ module Oddb2xml
           end
           xml.RESULT {
             xml.OK_ERROR   'OK'
-            xml.NBR_RECORD objects.length.to_s
+            xml.NBR_RECORD @articles.length.to_s
             xml.ERROR_CODE ''
             xml.MESSAGE    ''
           }
@@ -490,5 +627,52 @@ module Oddb2xml
       end
       _builder.to_xml
     end
+    def build_fi_product
+      prepare_products
+      _builder = Nokogiri::XML::Builder.new(:encoding => 'utf-8') do |xml|
+        xml.doc.tag_suffix = @tag_suffix
+        datetime = Time.new.strftime('%FT%T.%7N%z')
+        xml.KOMPENDIUM_PRODUCT(
+          'xmlns:xsd'         => 'http://www.w3.org/2001/XMLSchema',
+          'xmlns:xsi'         => 'http://www.w3.org/2001/XMLSchema-instance',
+          'xmlns'             => 'http://wiki.oddb.org/wiki.php?pagename=Swissmedic.Datendeklaration',
+          'CREATION_DATETIME' => datetime,
+          'PROD_DATE'         => datetime,
+          'VALID_DATE'        => datetime,
+        ) {
+          length = 0
+          %w[de fr].each do |lang|
+            info_index = {}
+            @infos[lang].each_with_index do |info, i|
+              info_index[info[:monid]] = i
+            end
+            # prod
+            @products.each do |seq|
+              seq[:packages].values.each do |pac|
+                if pac[:swissmedic_number] =~ /(\d{5})(\d{3})/
+                  number = $1.to_s
+                  if i = info_index[number]
+                    length += 1
+                    xml.KP('DT' => '') {
+                      xml.MONID @infos[lang][i][:monid]
+                      xml.PRDNO seq[:product_key] unless seq[:product_key].empty?
+                      # as orphans ?
+                      xml.DEL   @orphans.include?(number) ? true : false
+                    }
+                  end
+                end
+              end
+            end
+          end
+          xml.RESULT {
+            xml.OK_ERROR   'OK'
+            xml.NBR_RECORD length
+            xml.ERROR_CODE ''
+            xml.MESSAGE    ''
+          }
+        }
+      end
+      _builder.to_xml
+    end
   end
 end

data/lib/oddb2xml/cli.rb

@@ -9,39 +9,51 @@ require 'oddb2xml/compressor'
 module Oddb2xml
   class Cli
     SUBJECTS  = %w[product article]
-    ADDITIONS = %w[substance limitation]
-    OPTIONALS = %w[fi]
+    ADDITIONS = %w[substance limitation interaction code]
+    OPTIONALS = %w[fi fi_product]
     LANGUAGES = %w[DE FR] # EN does not exist
     def initialize(args)
       @options = args
       @mutex = Mutex.new
       @items = {} # Items from Preparations.xml in BAG
       @index = {} # Base index from swissINDEX
-      @infos = {} # FI from SwissmedicInfo
-      @orphans = [] # Orphaned drugs from Swissmedic xls
-      @fridges = [] # ReFridge drugs from Swissmedic xls
+      @infos = {} # [option] FI from SwissmedicInfo
+      @actions = [] # [addition] interactions from epha
+      @orphans = [] # [addition] Orphaned drugs from Swissmedic xls
+      @fridges = [] # [addition] ReFridge drugs from Swissmedic xls
       LANGUAGES.each do |lang|
         @index[lang] = {}
       end
     end
     def run
       threads = []
-      # swissmedic
-      threads << Thread.new do
-        downloader = SwissmedicInfoDownloader.new
-        xml = downloader.download
-        @mutex.synchronize do
-          hsh = SwissmedicInfoExtractor.new(xml).to_hash
-          @infos = hsh
+      # swissmedic-info
+      if @options[:fi]
+        threads << Thread.new do
+          downloader = SwissmedicInfoDownloader.new
+          xml = downloader.download
+          @mutex.synchronize do
+            hsh = SwissmedicInfoExtractor.new(xml).to_hash
+            @infos = hsh
+          end
         end
       end
+      # swissmedic
       [:orphans, :fridges].each do |type|
         threads << Thread.new do
-          downloader = SwissmedicDownloader.new
-          io = downloader.download_by(type)
+          downloader = SwissmedicDownloader.new(type)
+          io = downloader.download
           self.instance_variable_set("@#{type.to_s}", SwissmedicExtractor.new(io, type).to_arry)
         end
       end
+      # epha
+      threads << Thread.new do
+        downloader = EphaDownloader.new
+        io = downloader.download
+        @mutex.synchronize do
+          @actions = EphaExtractor.new(io).to_hash
+        end
+      end
       # bag
       threads << Thread.new do
         downloader = BagXmlDownloader.new
@@ -55,8 +67,8 @@ module Oddb2xml
         # swissindex
         types.each do |type|
           threads << Thread.new do
-            downloader = SwissIndexDownloader.new(type)
-            xml = downloader.download_by(lang)
+            downloader = SwissIndexDownloader.new(type, lang)
+            xml = downloader.download
             @mutex.synchronize do
               hsh = SwissIndexExtractor.new(xml, type).to_hash
               @index[lang][type] = hsh
@@ -85,8 +97,12 @@ module Oddb2xml
             builder.index   = index
             builder.items   = @items
             # additions
-            builder.orphans = @orphans
-            builder.fridges = @fridges
+            %w[actions orphans fridges].each do |addition|
+              builder.send("#{addition}=".intern, self.instance_variable_get("@#{addition}"))
+            end
+            #builder.actions = @actions
+            #builder.orphans = @orphans
+            #builder.fridges = @fridges
             # optionals
             builder.infos = @infos
             builder.tag_suffix = @options[:tag_suffix]
@@ -115,6 +131,11 @@ module Oddb2xml
     def files
       unless @_files
         @_files = {}
+        ##
+        # building order
+        #   1. addtions
+        #   2. subjects
+        #   3. optionals
         _files = (ADDITIONS + SUBJECTS)
         _files += OPTIONALS if @options[:fi]
         _files.each do|sbj|

data/lib/oddb2xml/downloader.rb

@@ -13,7 +13,11 @@ module Oddb2xml
       init
     end
     def init
-      # pass
+      @agent = Mechanize.new
+      @agent.user_agent = 'Mozilla/5.0 (X11; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0'
+      @agent.redirect_ok         = true
+      @agent.redirection_limit   = 5
+      @agent.follow_meta_refresh = true
     end
     protected
     def retrievable?
@@ -25,23 +29,39 @@ module Oddb2xml
         false
       end
     end
+    def read_xml_form_zip(target, zipfile)
+      xml = ''
+      if RUBY_PLATFORM =~ /mswin/i # for memory error
+        Zip::ZipFile.foreach(zipfile) do |entry|
+          if entry.name =~ target
+            entry.get_input_stream do |io|
+              while line = io.gets
+                xml << line
+              end
+            end
+          end
+        end
+      else
+        Zip::ZipFile.foreach(zipfile) do |entry|
+          if entry.name =~ target
+            entry.get_input_stream { |io| xml = io.read }
+          end
+        end
+      end
+      xml
+    end
   end
   class BagXmlDownloader < Downloader
     def init
+      super
       @url ||= 'http://bag.e-mediat.net/SL2007.Web.External/File.axd?file=XMLPublications.zip'
     end
     def download
       file = 'XMLPublications.zip'
       begin
-        response = Mechanize.new.get(@url)
+        response = @agent.get(@url)
         response.save_as file
-        xml = ''
-        Zip::ZipFile.foreach(file) do |entry|
-          if entry.name =~ /^Preparation/iu
-            entry.get_input_stream{ |io| xml = io.read }
-          end
-        end
-        return xml
+        return read_xml_form_zip(/^Preparation/iu, file)
       rescue Timeout::Error
         retrievable? ? retry : raise
       ensure
@@ -52,33 +72,33 @@ module Oddb2xml
     end
   end
   class SwissIndexDownloader < Downloader
-    def initialize(type=:pharma)
+    def initialize(type=:pharma, lang='DE')
       @type = (type == :pharma ? 'Pharma' : 'NonPharma')
+      @lang = lang
       url = "https://index.ws.e-mediat.net/Swissindex/#{@type}/ws_#{@type}_V101.asmx?WSDL"
       super(url)
     end
     def init
-      @config = {
+      config = {
         :log_level       => :info,
         :log             => false, # $stdout
         :raise_errors    => true,
         :ssl_verify_mode => :none,
         :wsdl            => @url
       }
+      @client = Savon::Client.new(config)
     end
-    def download_by(lang = 'DE')
-      client = Savon::Client.new(@config)
+    def download
       begin
-        type = @type
         soap = <<XML
 <?xml version="1.0" encoding="utf-8"?>
 <soap:Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/">
 <soap:Body>
-  <lang xmlns="http://swissindex.e-mediat.net/Swissindex#{type}_out_V101">#{lang}</lang>
+  <lang xmlns="http://swissindex.e-mediat.net/Swissindex#{@type}_out_V101">#{@lang}</lang>
 </soap:Body>
 </soap:Envelope>
 XML
-        response = client.call(:download_all, :xml => soap)
+        response = @client.call(:download_all, :xml => soap)
         if response.success?
           if xml = response.to_xml
             return xml
@@ -95,25 +115,26 @@ XML
     end
   end
   class SwissmedicDownloader < Downloader
-    HOST = 'http://www.swissmedic.ch'
-    def init
-    end
-    def download_by(index=:orphans)
-      case index
+    def initialize(type=:orphans)
+      @type = type
+      case @type
       when :orphans
-        @url ||= "#{HOST}/daten/00081/index.html?lang=de"
-        xpath =  "//div[@id='sprungmarke0_4']//a[@title='Humanarzneimittel']"
+        action = "daten/00081/index.html?lang=de"
+        @xpath = "//div[@id='sprungmarke0_4']//a[@title='Humanarzneimittel']"
       when :fridges
-        @url ||= "#{HOST}/daten/00080/00254/index.html?lang=de"
-        xpath =  "//table[@class='swmTableFlex']//a[@title='B3.1.35-d.xls']"
+        action = "daten/00080/00254/index.html?lang=de"
+        @xpath = "//table[@class='swmTableFlex']//a[@title='B3.1.35-d.xls']"
       end
-      file = "swissmedic_#{index}.xls"
+      url = "http://www.swissmedic.ch/#{action}"
+      super(url)
+    end
+    def download
+      file = "swissmedic_#{@type}.xls"
       begin
-        agent = Mechanize.new
-        page = agent.get(@url)
-        if link = page.search(xpath).first
-          url = HOST + link['href']
-          response = agent.get(url)
+        page = @agent.get(@url)
+        if link_node = page.search(@xpath).first
+          link = Mechanize::Page::Link.new(link_node, @agent, page)
+          response = link.click
           response.save_as file
         end
         return File.open(file, 'rb')
@@ -128,15 +149,15 @@ XML
   end
   class SwissmedicInfoDownloader < Downloader
     def init
+      super
+      @agent.ignore_bad_chunking = true
       @url ||= "http://download.swissmedicinfo.ch/Accept.aspx?ReturnUrl=%2f"
     end
     def download
       file = "swissmedic_info.zip"
       begin
         response = nil
-        agent = Mechanize.new
-        agent.ignore_bad_chunking = true
-        if home = agent.get(@url)
+        if home = @agent.get(@url)
           form = home.form_with(:id => 'Form1')
           bttn = form.button_with(:name => 'ctl00$MainContent$btnOK')
           if page = form.submit(bttn)
@@ -148,13 +169,7 @@ XML
         if response
           response.save_as file
         end
-        xml = ''
-        Zip::ZipFile.foreach(file) do |entry|
-          if entry.name =~ /^AipsDownload_/iu
-            entry.get_input_stream{ |io| xml = io.read }
-          end
-        end
-        return xml
+        return read_xml_form_zip(/^AipsDownload_/iu, file)
       rescue Timeout::Error
         retrievable? ? retry : raise
       rescue NoMethodError => e
@@ -166,4 +181,24 @@ XML
       end
     end
   end
+  class EphaDownloader < Downloader
+    def init
+      super
+      @url ||= 'http://community.epha.ch/interactions_de_utf8.csv'
+    end
+    def download
+      file = "epha_interactions.csv"
+      begin
+        response = @agent.get(@url)
+        response.save_as file
+        return File.open(file, 'r')
+      rescue Timeout::Error
+        retrievable? ? retry : raise
+      ensure
+        if File.exists? file
+          File.unlink file
+        end
+      end
+    end
+  end
 end

data/lib/oddb2xml/extractor.rb

@@ -200,4 +200,28 @@ module Oddb2xml
       data
     end
   end
+  class EphaExtractor < Extractor
+    def initialize(io)
+      @io = io
+    end
+    def to_hash
+      data = []
+      ixno = 0
+      while line = @io.gets
+        next if line =~ /^ATC1;Name1;ATC2;Name2;/
+        row = line.chomp.gsub("\"", '').split(';')
+        ixno += 1
+        action = {}
+        action[:ixno] = ixno
+        action[:atc1] = row[0]
+        action[:atc2] = row[2]
+        action[:mechanism] = row[5]
+        action[:effect]    = row[6]
+        action[:measures]  = row[7]
+        action[:grad]      = row[8]
+        data << action
+      end
+      data
+    end
+  end
 end

data/lib/oddb2xml/version.rb

@@ -1,3 +1,3 @@
 module Oddb2xml
-  VERSION = "1.1.2"
+  VERSION = "1.1.3"
 end

data/oddb2xml.gemspec

@@ -0,0 +1,30 @@
+# encoding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'oddb2xml/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "oddb2xml"
+  gem.version       = Oddb2xml::VERSION
+  gem.authors       = [""]
+  gem.email         = [""]
+  gem.description   = %q{TODO: Write a gem description}
+  gem.summary       = %q{TODO: Write a gem summary}
+  gem.homepage      = ""
+
+  gem.files         = `git ls-files`.split($/)
+  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 'rubyzip'
+  gem.add_dependency 'archive-tar-minitar'
+  gem.add_dependency 'mechanize'
+  gem.add_dependency 'nokogiri'
+  gem.add_dependency 'savon', '>= 2.0'
+  gem.add_dependency 'spreadsheet'
+
+  gem.add_development_dependency 'rspec'
+  gem.add_development_dependency 'webmock'
+  gem.add_development_dependency 'ZenTest'
+end

data/spec/cli_spec.rb

@@ -32,6 +32,7 @@ describe Oddb2xml::Cli do
       opts = {
         :compress_ext => 'tar.gz',
         :nonpharma    => false,
+        :fi           => false,
         :tag_suffix   => nil,
       }
       Oddb2xml::Cli.new(opts)
@@ -64,6 +65,7 @@ describe Oddb2xml::Cli do
       opts = {
         :compress_ext => 'zip',
         :nonpharma    => false,
+        :fi           => false,
         :tag_suffix   => nil,
       }
       Oddb2xml::Cli.new(opts)
@@ -96,6 +98,7 @@ describe Oddb2xml::Cli do
       opts = {
         :compress_ext => nil,
         :nonpharma    => true,
+        :fi           => false,
         :tag_suffix   => nil,
       }
       Oddb2xml::Cli.new(opts)
@@ -110,12 +113,20 @@ describe Oddb2xml::Cli do
       Dir.glob('oddb_*.tar.gz').first.should be_nil
       Dir.glob('oddb_*.zip').first.should be_nil
     end
-    it 'should create 2 xml files' do
+    it 'should create xml files' do
       $stdout.should_receive(:puts).with(/NonPharma/)
       cli.run
+      expected = [
+        'oddb_product.xml',
+        'oddb_article.xml',
+        'oddb_limitation.xml',
+        'oddb_substance.xml',
+        'oddb_interaction.xml',
+        'oddb_code.xml'
+      ].length
       Dir.glob('oddb_*.xml').each do |file|
         File.exists?(file).should be_true
-      end
+      end.to_a.length.should equal expected
     end
     after(:each) do
       Dir.glob('oddb_*.xml').each do |file|
@@ -128,6 +139,7 @@ describe Oddb2xml::Cli do
       opts = {
         :compress_ext => nil,
         :nonpharma    => false,
+        :fi           => false,
         :tag_suffix   => '_swiss'.upcase,
       }
       Oddb2xml::Cli.new(opts)
@@ -142,12 +154,20 @@ describe Oddb2xml::Cli do
       Dir.glob('oddb_*.tar.gz').first.should be_nil
       Dir.glob('oddb_*.zip').first.should be_nil
     end
-    it 'should create 2 xml files with prefix swiss_' do
+    it 'should create xml files with prefix swiss_' do
       $stdout.should_receive(:puts).with(/Pharma/)
       cli.run
+      expected = [
+        'swiss_product.xml',
+        'swiss_article.xml',
+        'swiss_limitation.xml',
+        'swiss_substance.xml',
+        'swiss_interaction.xml',
+        'swiss_code.xml'
+      ].length
       Dir.glob('swiss_*.xml').each do |file|
         File.exists?(file).should be_true
-      end
+      end.to_a.length.should equal expected
     end
     after(:each) do
       Dir.glob('swiss_*.xml').each do |file|
@@ -155,4 +175,47 @@ describe Oddb2xml::Cli do
       end
     end
   end
+  context 'when -o fi option is given' do
+    let(:cli) do
+      opts = {
+        :compress_ext => nil,
+        :nonpharma    => false,
+        :fi           => true,
+        :tag_suffix   => nil,
+      }
+      Oddb2xml::Cli.new(opts)
+    end
+    it_behaves_like 'any interface'
+    it 'should have nonpharma option' do
+      cli.should have_option(:fi => true)
+    end
+    it 'should not create any compressed file' do
+      $stdout.should_receive(:puts).with(/Pharma/)
+      cli.run
+      Dir.glob('oddb_*.tar.gz').first.should be_nil
+      Dir.glob('oddb_*.zip').first.should be_nil
+    end
+    it 'should create xml files' do
+      $stdout.should_receive(:puts).with(/Pharma/)
+      cli.run
+      expected = [
+        'oddb_fi.xml',
+        'oddb_fi_product.xml',
+        'oddb_product.xml',
+        'oddb_article.xml',
+        'oddb_limitation.xml',
+        'oddb_substance.xml',
+        'oddb_interaction.xml',
+        'oddb_code.xml'
+      ].length
+      Dir.glob('oddb_*.xml').each do |file|
+        File.exists?(file).should be_true
+      end.to_a.length.should equal expected
+    end
+    after(:each) do
+      Dir.glob('oddb_*.xml').each do |file|
+        File.unlink(file) if File.exists?(file)
+      end
+    end
+  end
 end

data/spec/compressor_spec.rb

@@ -9,6 +9,8 @@ shared_examples_for 'any compressor' do
     @compressor.contents << File.expand_path('../data/oddb_product.xml', __FILE__)
     @compressor.contents << File.expand_path('../data/oddb_substance.xml', __FILE__)
     @compressor.contents << File.expand_path('../data/oddb_limitation.xml', __FILE__)
+    @compressor.contents << File.expand_path('../data/oddb_fi.xml', __FILE__)
+    @compressor.contents << File.expand_path('../data/oddb_fi_product.xml', __FILE__)
     @compressor.finalize!.should == true
     compress_file = @compressor.instance_variable_get(:@compress_file)
     File.exists?(compress_file).should == true

data/spec/data/epha_interactions.csv

@@ -0,0 +1,3 @@
+ATC1;Name1;ATC2;Name2;Info;Mechanismus;Effekt;Massnahmen;Grad
+"N06AB06";"Sertralin";"M03BX02";"Tizanidin";"Keine Interaktion";"Tizanidin wird über CYP1A2 metabolisiert. Sertralin beeinflusst CYP1A2 jedoch nicht.";"Keine Interaktion.";"Die Kombination aus Sertralin und Tizanidin hat kein bekanntes Interaktionspotential.";"A"
+"J05AE08";"Atazanavir";"C10AA05";"Atorvastatin";"Erhöhtes Risiko für Myopathie und Rhabdomyolyse";"Atazanavir hemmt CYP3A4 und darüber auch den Abbau von Atorvastatin, was zu erhöhten Plasmakonzentrationen von Atorvastatin führt..";"Aufgrund der Inhibition von CYP3A4 durch Atazanavir kann die Atorvastatinkonzentration im Plasma ansteigen, was mit einem erhöhten Risiko für Myopathie und Rhabdomyolyse einhergeht.";"Kombination nach Möglichkeit meiden und alternativ Statin wählen, welches nicht mit Atazanavir interagiert, wie z.B. Pravastatin. Ist nach Nutzen-Risiko-Abwägung die Kombination aus Atorvastatin und Atazanavir erforderlich, niedrige Atorvastatindosis (z.B. 10 mg/d) wählen und auf Zeichen der Myopathie und Rhabdomyolyse, wie Muskelschwäche,  Muskelschmerzen, verfärbter Urin und CK-Anstieg, achten. Die Kombination aus Atazanavir und Ritonavir mit Atorvastatin ist kontraindiziert.";"D"

data/spec/data/swissmedic_info.html

@@ -5,6 +5,8 @@
   <title></title>
 </head>
 <body>
+  <form id="Form1" method="get" action="/Accept.aspx">
+    <input name="ctl00$MainContent$btnOK" value="1" />
+  </form>
 </body>
 </html>
-

data/spec/data/swissmedic_info_2.html

@@ -0,0 +1,13 @@
+<!DOCTYPE HTML>
+<html lang="utf-8">
+<head>
+  <meta charset="UTF-8">
+  <title></title>
+</head>
+<body>
+  <form id="Form1" method="get" action="/Accept.aspx">
+    <input name="ctl00$MainContent$BtnYes" value="1" />
+  </form>
+</body>
+</html>
+

data/spec/downloader_spec.rb

@@ -21,7 +21,7 @@ describe Oddb2xml::BagXmlDownloader do
   include ServerMockHelper
   before(:each) do
     setup_bag_xml_server_mock
-    @downloader = Oddb2xml::BagXmlDownloader.new()
+    @downloader = Oddb2xml::BagXmlDownloader.new
   end
   it_behaves_like 'any downloader'
   context 'when download is called' do
@@ -47,13 +47,13 @@ describe Oddb2xml::SwissIndexDownloader do
   before(:each) do
     setup_swiss_index_server_mock
   end
-  context 'Pharma' do
+  context 'Pharma with DE' do
     before(:each) do
-      @downloader = Oddb2xml::SwissIndexDownloader.new(:pharma)
+      @downloader = Oddb2xml::SwissIndexDownloader.new(:pharma, 'DE')
     end
     it_behaves_like 'any downloader'
     context 'when download_by is called with DE' do
-      let(:xml) { @downloader.download_by('DE') }
+      let(:xml) { @downloader.download }
       it 'should parse response hash to xml' do
         xml.should be_a String
         xml.length.should_not == 0
@@ -65,13 +65,13 @@ describe Oddb2xml::SwissIndexDownloader do
       end
     end
   end
-  context 'NonPharma' do
+  context 'NonPharma with FR' do
     before(:each) do
-      @downloader = Oddb2xml::SwissIndexDownloader.new(:nonpharma)
+      @downloader = Oddb2xml::SwissIndexDownloader.new(:nonpharma, 'FR')
     end
     it_behaves_like 'any downloader'
-    context 'when download_by is called with DE' do
-      let(:xml) { @downloader.download_by('DE') }
+    context 'when download_by is called with FR' do
+      let(:xml) { @downloader.download }
       it 'should parse response hash to xml' do
         xml.should be_a String
         xml.length.should_not == 0
@@ -83,36 +83,90 @@ describe Oddb2xml::SwissIndexDownloader do
       end
     end
   end
+end
 
 describe Oddb2xml::SwissmedicDownloader do
+  include ServerMockHelper
+  context 'orphans' do
+    before(:each) do
+      setup_swissmedic_server_mock
+      @downloader = Oddb2xml::SwissmedicDownloader.new(:orphans)
+    end
+    it_behaves_like 'any downloader'
+    context 'download_by for orphans xls' do
+      let(:io) { @downloader.download }
+      it 'should return valid IO' do
+        io.should be_a IO
+        io.bytes.should_not nil
+      end
+      it 'should clean up current directory' do
+        io.should_not raise_error(Timeout::Error)
+        File.exist?('oddb_orphans.xls').should be(false)
+      end
+    end
+  end
+  context 'fridges' do
+    before(:each) do
+      setup_swissmedic_server_mock
+      @downloader = Oddb2xml::SwissmedicDownloader.new(:fridges)
+    end
+    context 'download_by for fridges xls' do
+      let(:io) { @downloader.download }
+      it 'should return valid IO' do
+        io.should be_a IO
+        io.bytes.should_not nil
+      end
+      it 'should clean up current directory' do
+        io.should_not raise_error(Timeout::Error)
+        File.exist?('oddb_fridges.xls').should be(false)
+      end
+    end
+  end
+end
+
+describe Oddb2xml::SwissmedicInfoDownloader do
   include ServerMockHelper
   before(:each) do
-    setup_swissmedic_server_mock
-    @downloader = Oddb2xml::SwissmedicDownloader.new()
+    setup_swissmedic_info_server_mock
+    @downloader = Oddb2xml::SwissmedicInfoDownloader.new
   end
   it_behaves_like 'any downloader'
-  context 'download_by for orphans xls' do
-    let(:io) { @downloader.download_by(:orphans) }
-    it 'should return valid IO' do
-      io.should be_a IO
-      io.bytes.should_not nil
+  context 'when download is called' do
+    let(:xml) { @downloader.download }
+    it 'should parse zip to string' do
+      xml.should be_a String
+      xml.length.should_not == 0
+    end
+    it 'should return valid xml' do
+      xml.should =~ /xml\sversion="1.0"/
+      xml.should =~ /medicalInformations/
+      xml.should =~ /content/
     end
     it 'should clean up current directory' do
-      io.should_not raise_error(Timeout::Error)
-      File.exist?('oddb_orphans.xls').should be(false)
+      xml.should_not raise_error(Timeout::Error)
+      File.exist?('swissmedic_info.zip').should be(false)
     end
   end
-  context 'download_by for fridges xls' do
-    let(:io) { @downloader.download_by(:fridges) }
-    it 'should return valid IO' do
-      io.should be_a IO
-      io.bytes.should_not nil
+end
+
+describe Oddb2xml::EphaDownloader do
+  include ServerMockHelper
+  before(:each) do
+    setup_epha_server_mock
+    @downloader = Oddb2xml::EphaDownloader.new
+  end
+  it_behaves_like 'any downloader'
+  context 'when download is called' do
+    let(:xml) { @downloader.download }
+    it 'should read csv to IO Object' do
+      xml.should be_a IO
+      xml.bytes.should_not nil
     end
     it 'should clean up current directory' do
-      io.should_not raise_error(Timeout::Error)
-      File.exist?('oddb_fridges.xls').should be(false)
+      xml.should_not raise_error(Timeout::Error)
+      File.exist?('epha_interactions.csv').should be(false)
     end
   end
 end
 
-end
+

data/spec/spec_helper.rb

@@ -21,6 +21,7 @@ module ServerMockHelper
     setup_swiss_index_server_mock
     setup_swissmedic_server_mock
     setup_swissmedic_info_server_mock
+    setup_epha_server_mock
   end
   def setup_bag_xml_server_mock
     # zip
@@ -101,28 +102,56 @@ module ServerMockHelper
     stub_html_url = "http://download.swissmedicinfo.ch/Accept.aspx?ReturnUrl=%2f"
     stub_response = File.read(File.expand_path("../data/swissmedic_info.html", __FILE__))
     stub_request(:get, stub_html_url).
-      with(:headers => {
-        'Accept' => '*/*',
-        'Host'   => 'download.swissmedicinfo.ch',
-      }).
+      with(
+        :headers => {
+          'Accept' => '*/*',
+          'Host'   => 'download.swissmedicinfo.ch',
+        }).
+      to_return(
+        :status  => 200,
+        :headers => {'Content-Type' => 'text/html; charset=utf-8'},
+        :body    => stub_response)
+    # html (dummy 2)
+    stub_html_url = 'http://download.swissmedicinfo.ch/Accept.aspx?ctl00$MainContent$btnOK=1'
+    stub_response = File.read(File.expand_path("../data/swissmedic_info_2.html", __FILE__))
+    stub_request(:get, stub_html_url).
+      with(
+        :headers => {
+          'Accept' => '*/*',
+          'Host'   => 'download.swissmedicinfo.ch',
+        }).
       to_return(
         :status  => 200,
         :headers => {'Content-Type' => 'text/html; charset=utf-8'},
         :body    => stub_response)
     # zip
-    stub_zip_url = "http://download.swissmedicinfo.ch/"
+    stub_zip_url = 'http://download.swissmedicinfo.ch/Accept.aspx?ctl00$MainContent$BtnYes=1'
     stub_response = File.read(File.expand_path('../data/swissmedic_info.zip', __FILE__))
     stub_request(:get, stub_zip_url).
+      with(
+        :headers => {
+          'Accept'          => '*/*',
+          'Accept-Encoding' => 'gzip,deflate,identity',
+          'Host'            => 'download.swissmedicinfo.ch',
+        }).
+      to_return(
+        :status  => 200,
+        :headers => {'Content-Type' => 'application/zip; charset=utf-8'},
+        :body    => stub_response)
+  end
+  def setup_epha_server_mock
+    # csv
+    stub_csv_url = 'http://community.epha.ch/interactions_de_utf8.csv'
+    stub_response = File.read(File.expand_path('../data/epha_interactions.csv', __FILE__))
+    stub_request(:get, stub_csv_url).
       with(:headers => {
-        'Accept'          => '*/*',
-        'Accept-Encoding' => 'gzip,deflate,identity',
-        'Host'            => 'download.swisssmedicinfo.ch',
+        'Accept' => '*/*',
+        'Host'   => 'community.epha.ch',
       }).
       to_return(
         :status  => 200,
-        :headers => {'Content-Type' => 'application/zip; charset=utf-8'},
+        :headers => {'Content-Type' => 'text/csv; charset=utf-8'},
         :body    => stub_response)
-
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: oddb2xml
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-08 00:00:00.000000000 Z
+date: 2013-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &9807060 !ruby/object:Gem::Requirement
+  requirement: &19096920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: '3.10'
   type: :development
   prerelease: false
-  version_requirements: *9807060
+  version_requirements: *19096920
 - !ruby/object:Gem::Dependency
   name: hoe
-  requirement: &9806460 !ruby/object:Gem::Requirement
+  requirement: &19112720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,7 +32,7 @@ dependencies:
         version: '2.13'
   type: :development
   prerelease: false
-  version_requirements: *9806460
+  version_requirements: *19112720
 description: ''
 email:
 - yasaka@ywesee.com,  zdavatz@ywesee.com
@@ -59,11 +59,15 @@ files:
 - lib/oddb2xml/downloader.rb
 - lib/oddb2xml/extractor.rb
 - lib/oddb2xml/version.rb
+- oddb2xml.gemspec
 - spec/builder_spec.rb
 - spec/cli_spec.rb
 - spec/compressor_spec.rb
 - spec/data/XMLPublications.zip
+- spec/data/epha_interactions.csv
 - spec/data/oddb_article.xml
+- spec/data/oddb_fi.xml
+- spec/data/oddb_fi_product.xml
 - spec/data/oddb_limitation.xml
 - spec/data/oddb_product.xml
 - spec/data/oddb_substance.xml
@@ -74,6 +78,7 @@ files:
 - spec/data/swissmedic_fridges.xls
 - spec/data/swissmedic_info.html
 - spec/data/swissmedic_info.zip
+- spec/data/swissmedic_info_2.html
 - spec/data/swissmedic_orphans.html
 - spec/data/swissmedic_orphans.xls
 - spec/data/wsdl.xml