gtin2atc 0.1.5 → 0.1.6

checksums.yaml

@@ -1,7 +1,15 @@
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data/History.txt

@@ -1,5 +1,12 @@
+=== 0.1.6 10.03.2015
+
+* Adapted to changed delimiter
+* updated EPha URL for wido ATC download.
+
 === 0.1.5 04.03.2015
 
+* Splitted ddd into qty, unit, route of administration
+* Added exfactory and public price
 * Added optional second parameter to specify output file
 * Added output for dosis (name, unit, qty) for mono-preparations
 

data/lib/gtin2atc/builder.rb

@@ -15,6 +15,10 @@ module Gtin2atc
     AtcNotInBag           = 'atc not in bag'
     AtcDifferent          = 'atc differed'
     CsvOutputOptions      =  { :col_sep => ';', :encoding => 'UTF-8'}
+    Mesurements = [ 'g', 'kg', 'l', 'mg', 'ml', 'cm', 'GBq']
+    # see  Selection of units of WHO DDD guidelines
+    RouteOfAdministrations = ['Inhal', 'R', 'N', 'O', 'SL', 'P', 'V', 'TD']
+
     def initialize(opts)
       Util.set_logging(opts[:log])
       @output = opts[:output]
@@ -38,9 +42,9 @@ module Gtin2atc
     end
     def epha_atc_extractor
       data = {}
-      body = open('https://download.epha.ch/cleaned/atc.csv').read.force_encoding('UTF-8')
+      body = open('https://download.epha.ch/data/atc/atc.csv').read.force_encoding('UTF-8')
       Util.debug_msg "epha_atc_extractor is #{body.size} bytes long"
-      csv = CSV.new(body, { :headers => false, :col_sep => '|' } )
+      csv = CSV.new(body, { :headers => false, :col_sep => ',' } )
       csv.to_a.each{
         |line|
         data[line[0]] = line[2] if line[2]
@@ -137,6 +141,10 @@ module Gtin2atc
             gtin = gtin.to_i
             item[:gtin] = gtin
             item[:name] = seq.NameDe + " " +  pac.DescriptionDe
+            if pac.Prices
+              item[:exfactory_price] = pac.Prices.ExFactoryPrice.Price if pac.Prices.ExFactoryPrice
+              item[:public_price]    = pac.Prices.PublicPrice.Price if pac.Prices.PublicPrice
+            end
             data[gtin] = item
             Util.debug_msg "run_bag_extractor add #{item}" if $VERBOSE
           else
@@ -149,12 +157,44 @@ module Gtin2atc
       data
     end
 
+    # return [qty, unit, roa] for simple, valid ddd
+    # return [nil, nil, full_text] for structured DDDs like Standarddosis: 10 Tabletten oder 50 ml Mixtur
+    # a simple ddd is valid if meets the following three criteria
+    # first part is a float value
+    # second part is a unit e.g. ml
+    # third part is one or several (separated by ',') RouteOfAdministrations
+    def get_valid_ddd(full_text)
+      result =[nil, nil, full_text]
+      return result unless full_text
+      return result if full_text.index(';') # e.g. 0,12 g O,R; 18 mg P; 60 mg SL; 3 mg TD; 50 mg TD Gel; 12 mg P bezogen auf Testosteronundecanoat
+      return result if full_text.index(':') # e.g. Standarddosis: 10 Tabletten oder 50 ml Mixture
+      if full_text
+        parts = full_text.split(' ')
+        return result if parts.size > 3
+        qty = parts[0] ? parts[0].sub(',', '.').to_f : ''
+        if Mesurements.index(parts[1]) and qty != 0.0
+          roas = parts[2].split(',')
+          valid = roas.size > 0
+          roas.each{
+            |roa|
+            unless RouteOfAdministrations.index(roa)
+              valid = false
+              break
+            end
+          }
+          result =  [qty, parts[1], parts[2]] if valid
+        end
+      end
+      result
+    end
+
     def run(gtins_to_parse=[], output_name=nil)
       Util.debug_msg("run #{gtins_to_parse}")
       Util.debug_msg("@use_swissindex true")
       @oddb_calc = oddb_calc_xml_extractor
       @data_epha_atc = epha_atc_extractor
       @data_swissindex = swissindex_xml_extractor
+      @data_bag = bag_xml_extractor
       emitted_ids = []
       if @do_compare
         output_name =  File.join(Util.get_archive, 'gtin2atc_swissindex.csv')
@@ -163,21 +203,23 @@ module Gtin2atc
         output_name =  File.join(Util.get_archive, output_name)
       end
       CSV.open(output_name,'w+', CsvOutputOptions) do |csvfile|
-        csvfile << ["gtin", "ATC", 'pharmacode', 'description', 'daily drug dose', 'selling units']
+        csvfile << ["gtin", "ATC", 'pharmacode', 'description', 'exfactory_price', 'public_price', 'selling units', 'name', 'qty', 'unit', 'ddd:qty', 'ddd:unit', 'ddd:full_text']
         @data_swissindex.sort.each do |gtin, item|
           if @do_compare or gtins_to_parse.size == 0 or
             gtins_to_parse.index(gtin.to_s) or
             gtins_to_parse.index(item[:pharmacode].to_s)
             atc = item[:atc_code]
-            ddd = @data_epha_atc[atc]
+            ddd = get_valid_ddd(@data_epha_atc[atc])
             selling_units = @oddb_calc[gtin] ? @oddb_calc[gtin][:SELLING_UNITS] : nil
+            exfactory_price = @data_bag[gtin] ? @data_bag[gtin][:exfactory_price] : nil
+            public_price    = @data_bag[gtin] ? @data_bag[gtin][:public_price] : nil
             emitted_ids << gtin.to_i if gtin
             emitted_ids << item[:pharmacode].to_i if item[:pharmacode]
             if @oddb_calc[gtin] and @oddb_calc[gtin][:COMPOSITIONS]
               comp = @oddb_calc[gtin][:COMPOSITIONS].COMPONENT.first
-              csvfile << [gtin, atc, item[:pharmacode], item[:description], ddd, selling_units, comp.NAME, comp.QTY, comp.UNIT]
+              csvfile << [gtin, atc, item[:pharmacode], item[:description], exfactory_price, public_price, selling_units, comp.NAME, comp.QTY, comp.UNIT, ddd].flatten
             else
-              csvfile << [gtin, atc, item[:pharmacode], item[:description], ddd, selling_units]
+              csvfile << [gtin, atc, item[:pharmacode], item[:description], exfactory_price, public_price, selling_units, nil, nil, nil,  ddd].flatten
             end
           end
         end
@@ -194,7 +236,6 @@ module Gtin2atc
       msg = "swissindex: Could not find info for #{missing_ids.size} missing ids see file pharmacode_gtin_not_found.txt"
       Util.debug_msg(msg)
       return unless @do_compare
-      @data_bag = bag_xml_extractor
       output_name =  File.join(Util.get_archive, 'gtin2atc_bag.csv')
       CSV.open(output_name,'w+', CsvOutputOptions) do |csvfile|
         csvfile << ["gtin", "ATC", 'description']

data/lib/gtin2atc/version.rb

@@ -1,3 +1,3 @@
 module Gtin2atc
-  VERSION = "0.1.5"
+  VERSION = "0.1.6"
 end

data/spec/builder_spec.rb

@@ -21,6 +21,7 @@ end
 describe Gtin2atc::Builder do
   include ServerMockHelper
   CSV_NAME = 'gtin2atc.csv'
+  FERRO = '7680316440115;B03AA07;20244;FERRO-GRADUMET Depottabl;;;30;Ferrum(ii);105.0;mg;;;0,2 g O Fe2+'
   before(:each) do
     @savedDir = Dir.pwd
     FileUtils.makedirs Gtin2atc::WorkDir
@@ -50,8 +51,8 @@ describe Gtin2atc::Builder do
     inhalt = IO.readlines(filename)
     /^\d{13};\w{4}/.should match inhalt[1]
     # Packungsgrösse, Dosierung, DDD, Route of Administration
-    /^gtin;ATC;pharmacode;description;daily drug dose/.should match inhalt.first
-    /^7680316440115;B03AA07;20244;FERRO-GRADUMET Depottabl;0,2 g O Fe2\+;/.should match inhalt.join("\n")
+    /^gtin;ATC;pharmacode;description;exfactory_price;public_price;selling units;name;qty;unit;ddd:qty;ddd:unit;ddd:full_text/.should match inhalt.first
+    IO.read(filename).index(FERRO).should_not == nil
   end
 
   context 'when 20273 41803 (Pharmacodes) is given' do
@@ -101,8 +102,8 @@ describe Gtin2atc::Builder do
       check_csv(CSV_NAME)
       inhalt = IO.readlines(CSV_NAME)
       inhalt.size.should eq 2+1 # one header lines + two items
-      inhalt[1].chomp.should eq '7680147690482;N07BC02;41803;KETALGIN Inj Lös 10 mg/ml;25 mg O,P;'
-      inhalt[2].chomp.should eq '7680353660163;B03AE10;20273;KENDURAL Depottabl;;'
+      inhalt[1].chomp.should eq '7680147690482;N07BC02;41803;KETALGIN Inj Lös 10 mg/ml;;;;;;;25.0;mg;O,P'
+      inhalt[2].chomp.should eq '7680353660163;B03AE10;20273;KENDURAL Depottabl;;;;;;;;;'
     end
   end
 
@@ -208,10 +209,14 @@ describe Gtin2atc::Builder do
     it 'should contain dose for FERRO-GRADUMET Depottab' do
       oddb_calc_xml = File.expand_path(File.join( __FILE__, '../data/oddb_calc.xml'))
       FileUtils.cp(oddb_calc_xml, Gtin2atc::WorkDir, :verbose => false)
-      @res = buildr_capture(:stdout){ cli.run() }
+      # buildr_capture(:stdout){ cli.run() }
+      cli.run()
       check_csv(CSV_NAME)
-      inhalt = IO.readlines(CSV_NAME)
-      inhalt.index("7680316440115;B03AA07;20244;FERRO-GRADUMET Depottabl;0,2 g O Fe2+;30;Ferrum(ii);105.0;mg\n").should_not == nil
+      inhalt = IO.read(CSV_NAME)
+      puts inhalt
+      inhalt.index(FERRO).should_not == nil
+      inhalt.index('7680291520390;N02BE01;31532;BEN-U-RON Supp 250 mg Kind;;;;;;;;;"3 g O,P,R; 0,75 g O Kinder DDD; 0,375 g R Säuglings DDD; 0,75 g R Kinder DDD"').should_not == nil
+      inhalt.index('7680147700112;N07BC02;41826;KETALGIN Tabl 5 mg;;;;;;;25.0;mg;O,P').should_not == nil
     end
   end
 

data/spec/spec_helper.rb

@@ -53,7 +53,7 @@ module ServerMockHelper
   end
   def setup_epha_atc_server_mock
     # zip
-    stub_url = 'https://download.epha.ch/cleaned/atc.csv'
+    stub_url = 'https://download.epha.ch/data/atc/atc.csv'
     stub_response = File.read(File.join(Gtin2atc::SpecData, 'atc.csv'))
     stub_request(:get, stub_url).
           with(:headers => {'Accept'=>'*/*', 'User-Agent'=>'Ruby'}).

metadata

@@ -1,167 +1,167 @@
 --- !ruby/object:Gem::Specification
 name: gtin2atc
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
 platform: ruby
 authors:
 - Niklaus Giger, Zeno R.R. Davatz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-04 00:00:00.000000000 Z
+date: 2015-03-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.1.6
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.1.6
 - !ruby/object:Gem::Dependency
   name: mechanize
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 2.5.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 2.5.1
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.5.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.5.10
 - !ruby/object:Gem::Dependency
   name: savon
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 2.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 2.4.0
 - !ruby/object:Gem::Dependency
   name: rubyXL
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 3.3.0
 - !ruby/object:Gem::Dependency
   name: sax-machine
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: webmock
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: gtin2atc file with gtin, atc_code, pharmanr from input file with gtin
@@ -171,8 +171,8 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- ".gitignore"
-- ".travis.yml"
+- .gitignore
+- .travis.yml
 - Gemfile
 - History.txt
 - LICENSE
@@ -207,17 +207,17 @@ 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: 2.4.5
+rubygems_version: 2.3.0
 signing_key: 
 specification_version: 4
 summary: gtin2atc creates csv files with GTIN and ATC.