oddb2xml 2.0.7 → 2.0.8

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    MDg2MTM3NzVmZDE3MjhkNjg5ODc3Y2IxNGJkYzVmYTBhMTYyNGI2MQ==
+    YTFjMTAzMzFiNjM4ZDMwOTUwMjYyMDI1YTZjZThjODBkZjU3MGE2MQ==
   data.tar.gz: !binary |-
-    MmM2ZjRlNzA5NTYwNWIzZDc0MTZmNjcwZDA1NWZkOGEyYzY2MDY2NQ==
+    Y2JhOTEzZmE0MmI1YTc1NDRjZjVhNDVmMWM0YzEzMjk0ZDc5NzliYw==
 SHA512:
   metadata.gz: !binary |-
-    Y2I2YTc2MjA0OTQ1MmFhMDEyZjBmNTZkY2IwMjVjNTg0MzQ1NzY4ZGRlYzIx
-    ZjY4OTAxNzRhMGVjYjU3OTMxYjg1YzVhNjQ0MmQzZTIxNzQwMzAyYTM2MDFj
-    M2ExZmFiZGU3NWRlN2U3YzBjOGE3MDNkMjJkMWQwNTAyNDViYjE=
+    ZjEyZGJiNGRjYzI0N2IzNjg0MDRmYWUwNTk4MDI0ZDdhMGYzMjMxMjdlNDRl
+    NWMzMjdiNDRhMGQ1NzQyYWI1ZmVlMTNhNmI1NTk3ZDk1MWVlZmFkNDM1MDIx
+    YzMxZjczYTZjYTBmYmY0YWQ4ZmZlYjExYjQyNzRhYTdkZTA2OWQ=
   data.tar.gz: !binary |-
-    ZjJkZDk1ZjIzOTVlODQ2YWU3MWE0ZmZkMGM3NTMyMTA2ODNlZGJlOWViOTJm
-    OTYyOTdkMTc0ODkyNTViNjI1Y2YzZDhlOGUyOWE4YzZhNzMzODlkNmQ1M2Jj
-    YmMzODcwMWRjMjIwNGVlOTkzZWMyMTJhZjQ3NDhhZmMyNjQ0ZjA=
+    ZjZjMzE1NjMxYzMyZjUwZjc3YThhZjRlMzY5ZTVjYzliOGFkYjJkZWMwNWU3
+    MzQ3ZjZmNDM4NjdhZDY3ZTUzZGM3ZThjNGE3MTUzYjU0ZjQ2YmMxMjhhOGUy
+    MmJkOTNhZDdlMjhiYjEyZmM5ODY5NWVkNDVjNThmNjhmNzZhMDE=

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    oddb2xml (2.0.7)
+    oddb2xml (2.0.8)
       archive-tar-minitar (~> 0.5.2)
       mechanize (~> 2.5.1)
       nokogiri (~> 1.5.10)

data/History.txt

@@ -1,3 +1,9 @@
+=== 2.0.8 / 29.04.2015
+
+* --calc.
+** Fixed adding substances instead of a way too long label_description, eg. 7680616310019 Moviprep Orange, Pulver
+** emit EXCIPIENS for each composition
+
 === 2.0.7 / 29.04.2015
 
 * parse swissmedic composition with the help of RubyGem parslet.

data/lib/oddb2xml/builder.rb

@@ -712,6 +712,7 @@ module Oddb2xml
               xml.COMPOSITIONS {
                 info.compositions.each { |composition|
                   xml.COMPOSITION {
+                    xml.EXCIPIENS { emit_substance(xml, composition.excipiens) } if composition.excipiens
                     xml.CORRESP composition.corresp if composition.corresp
                     xml.LABEL composition.label if composition.label
                     xml.LABEL_DESCRIPTION composition.label_description if composition.label_description

data/lib/oddb2xml/compositions_syntax.rb

@@ -296,8 +296,7 @@ class CompositionParser < Parslet::Parser
                       }
 
   rule(:excipiens)  { substance_lead.maybe.as(:more_info) >> space? >>
-                      ( excipiens_dose | excipiens_identifiers.as(:excipiens_description)) >>
-                      space? >> excipiens_dose.maybe.as(:dose_2) >>
+                      ( excipiens_dose | (excipiens_identifiers >> any.repeat(0)).as(:excipiens_description)) >>
                       any.repeat(0)
                     }
 
@@ -419,14 +418,17 @@ class CompositionParser < Parslet::Parser
 
   rule(:polvac) { label_id.as(:label) >> label_separator >> space? >> composition.as(:composition) >> space? >> str('.').maybe >> space? }
 
-  rule(:label_composition) { label >> space? >> composition.as(:excipiens) >> space? >> str('.').maybe >> space? }
   rule(:label_comment_excipiens) { label >> space? >> excipiens.as(:excipiens) >> space? >> str('.').maybe >> space? }
 
+  rule(:label_id_composition) { label_id.as(:label) >> label_separator >>
+                                ((space >> identifier).repeat(1) >> str(':')).maybe.as(:label_description) >>
+                                composition.as(:composition)  }
+
   rule(:expression_comp) {
+    multiple_et_line |
+    label_id_composition |
     corresp_line_neu |
     leading_label.maybe >> space? >> composition.as(:composition) >> space? >> str('.').maybe >> space? |
-    multiple_et_line |
-    label_composition |
     polvac |
     label_comment_excipiens |
     excipiens.as(:composition) |

data/lib/oddb2xml/parslet_compositions.rb

@@ -10,7 +10,7 @@ require 'parslet'
 require 'parslet/convenience'
 require 'oddb2xml/compositions_syntax'
 include Parslet
-VERBOSE_MESSAGES = false
+VERBOSE_MESSAGES ||= false
 
 module ParseUtil
   # this class is responsible to patch errors in swissmedic entries after
@@ -51,7 +51,7 @@ module ParseUtil
         result = result.gsub(entry.pattern,  entry.replacement)
         unless result.eql?(intermediate)
             entry.nr_occurrences += 1
-            puts "#{File.basename(__FILE__)}:#{__LINE__}: fixed \nbefore: #{intermediate}\nafter:  #{result}"
+            puts "#{File.basename(__FILE__)}:#{__LINE__}: fixed \nbefore: #{intermediate}\nafter:  #{result}" unless defined?(RSpec)
         end
       }
       @nrLines += 1
@@ -156,12 +156,17 @@ class CompositionTransformer < Parslet::Transform
     |dictionary|
       puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
       info = dictionary[:excipiens].is_a?(Hash) ? dictionary[:excipiens] : dictionary[:excipiens].first
-      @@excipiens           =  ParseSubstance.new(info[:excipiens_description] ? info[:excipiens_description] : 'Excipiens')
-      @@excipiens.dose      = info[:dose] if info[:dose]
-      @@excipiens.more_info = CompositionTransformer.get_ratio(dictionary)
-      @@excipiens.cdose     = info[:dose_corresp] if info[:dose_corresp]
-      @@excipiens.more_info = info[:more_info] if info[:more_info]
-      binding.pry if dictionary[:dose_2]
+      if info[:excipiens_description] or
+       info[:dose] or
+       info[:dose_corresp] or
+       info[:more_info] or
+       CompositionTransformer.get_ratio(dictionary)
+        @@excipiens           =  ParseSubstance.new(info[:excipiens_description] ? info[:excipiens_description] : 'Excipiens')
+        @@excipiens.dose      = info[:dose] if info[:dose]
+        @@excipiens.more_info = CompositionTransformer.get_ratio(dictionary)
+        @@excipiens.cdose     = info[:dose_corresp] if info[:dose_corresp]
+        @@excipiens.more_info = info[:more_info] if info[:more_info]
+      end
       nil
   }
   rule(:composition => subtree(:composition),
@@ -416,7 +421,7 @@ class ParseComposition
       if label and not /((A|B|C|D|E|I|II|III|IV|\)+)\s+et\s+(A|B|C|D|E|I|II|III|IV|\))+)/.match(label)
         result.label  = label
       end
-      result.label_description = label_description
+      result.label_description = label_description.gsub(/:+$/, '').strip if label_description
     end
     return result
   end

data/lib/oddb2xml/version.rb

@@ -1,3 +1,3 @@
 module Oddb2xml
-  VERSION = "2.0.7"
+  VERSION = "2.0.8"
 end

data/spec/calc_spec.rb

@@ -343,6 +343,10 @@ if RunAllTests
       XPath.match( doc, "//ARTICLE[GTIN='7680611860045']/NAME").first.text.should eq 'Nutriflex Omega special, Infusionsemulsion 2500 ml'
       XPath.match( doc, "//ARTICLE[GTIN='7680611860045']/SELLING_UNITS").first.text.should eq '5'
 
+      XPath.match( doc, "//ARTICLE[GTIN='7680165980114']/COMPOSITIONS/COMPOSITION/EXCIPIENS/SUBSTANCE_NAME").first.text.should eq 'Excipiens ad solutionem'
+      XPath.match( doc, "//ARTICLE[GTIN='7680165980114']/COMPOSITIONS/COMPOSITION/EXCIPIENS/QTY").first.text.should eq '1'
+      XPath.match( doc, "//ARTICLE[GTIN='7680165980114']/COMPOSITIONS/COMPOSITION/EXCIPIENS/UNIT").first.text.should eq 'ml'
+      XPath.match( doc, "//ARTICLE[GTIN='7680165980114']/NAME").first.text.should eq 'W-Tropfen'
     end
   end
 

data/spec/composition_syntax_spec.rb

@@ -9,7 +9,7 @@ RunAllParsingExamples = false # Takes over 3 minutes to run, all the other ones
 GoIntoPry = true
 NoGoIntoPry = false
 
-if GoIntoPry
+if NoGoIntoPry
 
 describe CompositionParser do
 let(:parser) { CompositionParser.new }
@@ -28,29 +28,14 @@ let(:parser) { CompositionParser.new }
     it "parses identifier" do
       res1 = substance_parser.parse_with_debug('pollinis allergeni extractum (alnus glutinosa, betula alba, corylus avellana) 300 U.: excipiens ad solutionem pro 1 ml')
       pp res1
-      binding.pry
-    res1 = excipiens_parser.parse_with_debug "excipiens ad emulsionem pro 1 g"
-      pp res1
-      binding.pry
-    res1 = substance_parser.parse_with_debug "excipiens ad emulsionem pro 1 g"
-      pp res1
-      binding.pry
-    res2 = substance_parser.parse_with_debug "excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi"
-      pp res2
-      binding.pry
-   res1 = substance_name_parser.parse_with_debug("argenti nitras aquos. D13")
-
-      string =
-"chlorhexidini digluconas 1 mg, aromatica, color.: corresp. ethanolum 8.5 % V/V, E 127, excipiens ad solutionem pro 1 ml"
-    res2 = composition_parser.parse_with_debug(string)
-    res2 = substance_parser.parse_with_debug(string)
-      pp res1
+      # binding.pry
     end
   end
 end
 else
 
 excipiens_tests = {
+  'aqua ad iniectabilia ad solutionem pro 4 ml' => nil,
   'aether q.s. ad solutionem pro 1 g' => 'aether q.s. ad solutionem',
   'saccharum ad globulos pro 1 g'  => 'saccarum',
   'q.s. ad solutionem pro 5 ml' => 'q.s. ad solutionem pro 5 ml',
@@ -71,8 +56,6 @@ excipiens_tests = {
 }
 
 substance_tests = {
-  'pollinis allergeni extractum (alnus glutinosa, betula alba, corylus avellana) 300 U.: excipiens ad solutionem pro 1 ml' => 'zzz',
-  'pollinis allergeni extractum (alnus glutinosa, betula alba, corylus avellana)' => 'xxx',
   "U = Histamin Equivalent Prick" => 'U = Histamin Equivalent Prick', # 58566
   "Vipera aspis > 1000 LD50 mus et Vipera berus > 500 LD50, natrii chloridum" => "Vipera Aspis > 1000 Ld50 Mus",
   "Vipera aspis > 1000 LD50 mus et Vipera berus > 500 LD50, natrii chloridum, polysorbatum 80" => "Vipera Aspis > 1000 Ld50 Mus",
@@ -80,7 +63,6 @@ substance_tests = {
   "Vipera aspis > 1000 LD50 mus et Vipera berus > 500 LD50, natrii chloridum, polysorbatum 80, aqua ad iniectabilia q.s. ad solutionem pro 4 ml" => "Vipera Aspis > 1000 Ld50 Mus",
   "antitoxinum equis Fab'" => "Antitoxinum Equis Fab'",
   "antitoxinum equis Fab'x" => "Antitoxinum Equis Fab'x",
-  "aqua ad iniectabilia ad solutionem pro 4 ml" => nil,# "Aqua Ad Iniectabilia Ad Solutionem Pro",
   "calcii gluconas 100 mg corresp. calcium 100 mg" => 'Calcii Gluconas',
   "calcii gluconas 100 mg et calcii lactas pentahydricus 25 mg et calcii hydrogenophosphas anhydricus 300 mg corresp. calcium 100 mg" => 'Calcii Gluconas',
   "calcii gluconas 100 mg et calcii lactas pentahydricus 25 mg et calcii hydrogenophosphas anhydricus 300 mg" => 'Calcii Gluconas',
@@ -93,8 +75,6 @@ substance_tests = {
   "conserv.: E 217, E 219, natrii dehydroacetas" => "E 217",
   "conserv.: E 217, E 219, natrii dehydroacetas, excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi" => "line #{__LINE__}",
   "ethanolum 59.5 % V/V" => 'Ethanolum',
-  "excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi" => "Excipiens Ad Solutionem Pro 1 Ml Corresp. 50 µg Pro Dosi",
-  "excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi" => "line #{__LINE__}",
   "globulina equina (immunisé')" => "Globulina Equina (immunisé')",
   "globulina equina (immunisé)" => 'Globulina Equina (immunisé)',
   "globulina equina'" => "Globulina Equina'",
@@ -124,7 +104,6 @@ substance_tests = {
   'benzoe 40 ml' => 'Benzoe',
   'color.: E 160(a)' => 'E 160', # TODO: or E 160(a) ??
   'ethanolum 70-78 % V/V' => "Ethanolum",
-  'excipiens ad solutionem pro 1 ml' => "Ad Solutionem Pro",
   'ginseng extractum corresp. ginsenosidea 3.4 mg' => 'Ginseng Extractum Corresp. Ginsenosidea',
   'moelle épinière' => 'Moelle épinière',
   'pimpinellae radix 15 % ad pulverem' => 'Pimpinellae Radix',
@@ -172,8 +151,6 @@ composition_tests = [
   "color.: E 160(a)\n",
   "conserv.: E 217, E 219, natrii dehydroacetas",
   "conserv.: E 217, E 219, natrii dehydroacetas, excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi.",
-  "excipiens ad emulsionem pro 1 g.\n",
-  "excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi.",
   "extractum ethanolicum et glycerolicum liquidum ex absinthii herba 0.7 mg, cinnamomi cortex 3.8 mg, guaiaci lignum 14.3 mg, millefolii herba 7 mg, rhoeados flos 11 mg, tormentillae rhizoma 9.5 mg, balsamum tolutanum 0.3 mg, benzoe tonkinensis 4.8 mg, myrrha 2.4 mg, olibanum 0.9 mg, excipiens ad solutionem pro 1 ml, corresp. 40 guttae, corresp. ethanolum 37 % V/V",
   "hamamelis virginiana D1 0,22 mg, hepar sulfuris D6 2,2 mg hypericum perforatum D2 0,66 mg, mercurius solubilis hahnemanni D8 1,1 mg, symphytum officinale D6 2,2 mg, aqua ad iniectabilia, natrii chloridum q.s. ad solutionem pro 2,2 ml.\n",
   "hepar sulfuris D6 2,2 mg hypericum perforatum D2 0,66 mg",
@@ -188,7 +165,6 @@ composition_tests = [
   "sennae folium 75 % corresp. hydroxyanthracenae 2.7 %",
   "viperis antitoxinum equis F(ab')2 corresp. Vipera aspis > 1000 LD50 mus et Vipera berus > 500 LD50 mus et Vipera ammodytes > 1000 LD50 mus, natrii chloridum, polysorbatum 80, aqua ad iniectabilia q.s. ad solutionem pro 4 ml.",
   "xylometazolini hydrochloridum 0.5 mg, natrii hyaluronas, conserv.: E 217, E 219, natrii dehydroacetas, excipiens ad solutionem pro 1 ml corresp. 50 µg pro dosi.",
-  'excipiens ad pulverem corresp. suspensio reconstituta 1 ml',
   'gasum inhalationis, pro vitro',
   'toxoidum pertussis 25 µg et haemagglutininum filamentosum 25 µg',
   'xenonum 74 -740 MBq',

data/spec/parslet_spec.rb

@@ -5,18 +5,18 @@ require 'pry'
 rescue LoadError
 end
 require 'pp'
+VERBOSE_MESSAGES = false
 require 'spec_helper'
 require "#{Dir.pwd}/lib/oddb2xml/parslet_compositions"
 require 'parslet/rig/rspec'
 
 hostname = Socket.gethostbyname(Socket.gethostname).first
-RunAllCompositionsTests = /travis|localhost/i.match(hostname) != nil # takes about five minutes to run!
+RunAllCompositionsTests = false # /travis|localhost/i.match(hostname) != nil # takes about five minutes to run!
 puts "hostname is #{hostname} RunAllCompositionsTests #{RunAllCompositionsTests}"
 # Testing whether 8937 composition lines can be parsed. Found 380 errors in 293 seconds
 # 520 examples, 20 failures, 1 pending
 
 RunFailingSpec = true
-  VERBOSE_MESSAGES = true
 
 describe ParseComposition do
 to_add = %(
@@ -44,6 +44,43 @@ end
 end
 
 describe ParseComposition do
+  context "should handle excipiens" do
+    string = "conserv.: E 216, E 218, excipiens pro suppositorio."
+    composition = ParseComposition.from_string(string)
+    specify { expect( composition.substances.size).to eq 2 }
+    specify { expect( composition.label).to eq nil }
+    specify { expect( composition.excipiens.name).to match /excipiens pro suppositorio/i }
+    specify { expect( composition.substances.first.name).to eq "E 216" }
+  end
+
+  context "should return label with description" do
+    string = "I) Glucoselösung: glucosum anhydricum 240 g ut glucosum monohydricum, calcii chloridum dihydricum 600 mg, acidum citricum monohydricum, aqua ad iniectabilia q.s. ad solutionem pro 500 ml."
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.substances.size).to eq 3 }
+    specify { expect(composition.label).to eq 'I' }
+    specify { expect(composition.label_description).to eq 'Glucoselösung' }
+  end
+
+  context "should handle label-description for Cyclacur" do
+    # 37987 1   Cyclacur, Dragées
+    string = "I) Weisse Dragées: estradioli valeras 2 mg, excipiens pro compresso obducto."
+    composition = ParseComposition.from_string(string)
+    specify { expect( composition.substances.size).to eq 1 }
+    specify { expect( composition.label).to eq 'I' }
+    specify { expect( composition.label_description).to eq "Weisse Dragées" }
+    specify { expect( composition.substances.first.name).to eq "Estradioli Valeras" }
+  end
+
+  context "should handle label-description for Moviprep" do
+    # 61631   1   Moviprep Orange, Pulver
+    string = "A): macrogolum 3350 100 g, natrii sulfas anhydricus 7.5 g, natrii chloridum 2.691 g, kalii chloridum 1.015 g, arom.: aspartamum et alia, excipiens ad pulverem pro charta."
+    composition = ParseComposition.from_string(string)
+    specify { expect( composition.substances.size).to eq 6 }
+    specify { expect( composition.label).to eq 'A' }
+    specify { expect( composition.label_description).to eq nil }
+    specify { expect( composition.substances.first.name).to eq "Macrogolum 3350" }
+  end
+
   context "should handle 'LA 2x%" do
     # 48473 1   Wala Echinacea-Mundspray, anthroposophisches Arzneimittel
     string = "echinacea pallida ex herba LA 20% TM 10 g"
@@ -1332,19 +1369,6 @@ describe ParseUtil::HandleSwissmedicErrors do
     specify { expect(handler.report[1].index(replacement).class).to eq Fixnum }
   end
 
-  context 'should be used when calling ParseComposition' do
-    replacement = '\1, \2'
-    test_string = 'sulfuris D6 2,2 mg hypericum perforatum D2 0,66'
-    report = ParseComposition.reset
-    composition = ParseComposition.from_string(test_string).clone
-    report = ParseComposition.report
-    specify { expect(composition.substances.size).to eq 2 }
-    specify { expect(composition.substances.first.name).to eq 'Sulfuris D6' }
-    specify { expect(composition.substances.last.name).to eq 'Hypericum Perforatum D2' }
-    specify { expect(/report/i.match(report[0]).class).to eq MatchData }
-    specify { expect(report[1].index(replacement).class).to eq Fixnum }
-  end
-
   end
 end
 

data/test_options.rb

@@ -48,6 +48,7 @@ prepare_for_gem_test
 # we will skip some long running tests as travis jobs must finish in less than 50 minutes
 # unfortunately it returns a very common name
 unless 'localhost.localdomain'.eql?(Socket.gethostbyname(Socket.gethostname).first)
+  test_one_call('oddb2xml --calc')
   test_one_call('oddb2xml -e')
   test_one_call('oddb2xml -e -I80')
   test_one_call('oddb2xml -f dat --append -I 80')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: oddb2xml
 version: !ruby/object:Gem::Version
-  version: 2.0.7
+  version: 2.0.8
 platform: ruby
 authors:
 - Yasuhiro Asaka, Zeno R.R. Davatz