oddb2xml 2.7.4 → 2.7.5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 1f4faf8f73b2cffa14bd3dda23dad4e401b524587c0f95d80e0cc9cbd4ba5d2b
+  metadata.gz: 2b92ef261a1ad3ea6a8e2ce6d60302b0acf4c50efe1897ec9379633d31c5cced
+  data.tar.gz: ebaca1d2e02274a59b416e407a1049662564b48abb474f28de50b00f5b250147
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+  data.tar.gz: 3a41d7685173bc57d9dfd0618f179ac0405140d203b50b2e750a97ebe438d2a285858972e081724d1ab525f4f106b22b7b673d2fa5511790b87287eac8e5609b

data/.github/workflows/ruby.yml

@@ -22,8 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu]
-        ruby: [2.5, 2.6, 2.7, 3.0, head]
-    continue-on-error: ${{ endsWith(matrix.ruby, 'head') }}
+        ruby: [2.6, 2.7, "3.0", 3.1]
     steps:
     - uses: actions/checkout@v2
     - uses: ruby/setup-ruby@v1

data/History.txt

@@ -1,3 +1,10 @@
+=== 2.7.5 / 1.02.2022
+* Specify old versions of savon and rdoc to avoid importing psych
+* Added ruby 3.1 to tested ruby versions
+* Removed ruby 2.5 from supported versions
+* Force psych to < 4.0 to avoid the error Psych::DisallowedClass: Tried to load unspecified class: Struct::GalenicGroup
+*   Therefor rdoc < 6.4
+
 === 2.7.4 / 30.03.2021
 * Update needed Ruby-Version to 2.5.0 in gemspec
 * Ensure downloads directory is created at first run

data/lib/oddb2xml/compositions_syntax.rb

@@ -213,7 +213,6 @@ class CompositionParser < Parslet::Parser
       str("et ") |
       str("excipiens") |
       str("partes") |
-      str("pro capsula") |
       str("pro dosi") |
       str("pro vitroe") |
       str("q.s. ad ") |
@@ -259,6 +258,9 @@ class CompositionParser < Parslet::Parser
 
   rule(:pro_identifiers) {
     str("ut aqua ad iniectabilia q.s. ad emulsionem pro ") |
+      str("aqua ").maybe >> str("ad iniectabile q.s. ad suspensionem pro ") |
+      str("aqua ").maybe >> str("ad iniectabile q.s. ad solutionem pro ") |
+      str("aqua ").maybe >> str("ad iniectabile ad solutionem pro ") |
       str("aqua ").maybe >> str("ad iniectabilia q.s. ad solutionem pro ") |
       str("aqua ").maybe >> str("ad solutionem pro ") |
       str("aqua ").maybe >> str("q.s. ad emulsionem pro ") |
@@ -270,6 +272,7 @@ class CompositionParser < Parslet::Parser
       str("excipiens ad pulverem pro ") |
       str("excipiens ad solutionem pro ") |
       str("pro vase ") |
+      str("pro capsula ") |
       str("q.s. ad pulverem pro ")
   }
   rule(:excipiens_dose) {

data/lib/oddb2xml/downloader.rb

@@ -243,7 +243,7 @@ module Oddb2xml
   class RefdataDownloader < Downloader
     def initialize(options = {}, type = :pharma)
       @type = (type == :pharma ? "Pharma" : "NonPharma")
-      url = "http://refdatabase.refdata.ch/Service/Article.asmx?WSDL"
+      url = "https://refdatabase.refdata.ch/Service/Article.asmx?WSDL"
       super(options, url)
     end
 

data/lib/oddb2xml/parslet_compositions.rb

@@ -6,7 +6,7 @@
 
 require "parslet"
 require "parslet/convenience"
-require "oddb2xml/compositions_syntax"
+require_relative "compositions_syntax"
 VERBOSE_MESSAGES ||= false
 
 module ParseUtil
@@ -101,6 +101,7 @@ module ParseUtil
   rescue => error
     puts "error #{error}"
     # binding.pry
+    raise error
   end
 end
 
@@ -373,6 +374,7 @@ class ParseComposition
   ERRORS_TO_FIX = {
     /(\d+)\s+-\s*(\d+)/ => '\1-\2',
     "o.1" => "0.1",
+    /polymerisat(i|um) \d:\d/ => "polymerisatum",
     /\s+(mg|g) DER:/ => ' \1, DER:',
     " mind. " => " min. ",
     " streptococci pyogen. " => " streptococci pyogen ",
@@ -384,7 +386,7 @@ class ParseComposition
     / U\.: (excipiens) / => ' U. \1 ',
     / U\.: (alnus|betula|betula|betulae) / => ' U., \1 ',
     /^(acari allergeni extractum (\(acarus siro\)|).+\s+U\.:)/ => 'A): \1',
-    "Solvens: alprostadilum" => "alprostadilum"
+    "Solvens: alprostadilum" => "alprostadilum",
   }
   @@error_handler = ParseUtil::HandleSwissmedicErrors.new(ERRORS_TO_FIX)
 

data/lib/oddb2xml/version.rb

@@ -1,3 +1,3 @@
 module Oddb2xml
-  VERSION = "2.7.4"
+  VERSION = "2.7.5"
 end

data/oddb2xml.gemspec

@@ -24,7 +24,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency "minitar" # , '~> 0.5.2'
   spec.add_dependency "mechanize" # , '~> 2.5.1'
   spec.add_dependency "nokogiri", ">= 1.8.2"
-  spec.add_dependency "savon" # , '~> 2.11.0'
+  spec.add_dependency "savon" , '~> 2.12.0'
   spec.add_dependency "spreadsheet" # , '~> 1.0.0'
   spec.add_dependency "rubyXL", "~> 3.4.0"
   spec.add_dependency "sax-machine" # ,  '~> 0.1.0'
@@ -44,8 +44,9 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "rake"
   spec.add_development_dependency "rspec"
   spec.add_development_dependency "webmock"
-  spec.add_development_dependency "rdoc"
+  spec.add_development_dependency "rdoc", "~> 6.3.3" # rdoc 6.4 depends on psych 4.0 which breaks savon!
   spec.add_development_dependency "vcr"
   spec.add_development_dependency "timecop"
   spec.add_development_dependency "flexmock"
+  spec.add_development_dependency "psych", "< 4.0.0"
 end

data/shell.nix

@@ -0,0 +1,17 @@
+# See https://nixos.wiki/wiki/Packaging/Ruby
+# A small helper script to get a development version for oddb2xml under NixOS
+with import <nixpkgs> {};
+stdenv.mkDerivation {
+  name = "env";
+  buildInputs = [
+    ruby_3_0.devEnv
+    git
+    python
+    libpcap
+    libxml2
+    libxslt
+    pkg-config
+    bundix
+    gnumake
+  ];
+}

data/spec/builder_spec.rb

@@ -546,7 +546,8 @@ describe Oddb2xml::Builder do
     it "should flag fridge drugs correctly" do
       doc = REXML::Document.new IO.read(checkAndGetArticleXmlName)
       checkAndGetArticleWithGTIN(doc, Oddb2xml::FRIDGE_GTIN)
-      expect(REXML::XPath.match(doc, "//COOL='1']").size).to eq 1
+      expect(REXML::XPath.match(doc, "//COOL=").size).to eq 1
+      expect(REXML::XPath.match(doc, "//COOL").first.text).to eq "1"
     end
 
     ean_with_drug_index = 7680555610041

data/spec/fixtures/vcr_cassettes/oddb2xml.json

@@ -19,7 +19,7 @@
                     ]
                 },
                 "method": "get",
-                "uri": "http://refdatabase.refdata.ch/Service/Article.asmx?WSDL"
+                "uri": "https://refdatabase.refdata.ch/Service/Article.asmx?WSDL"
             },
             "response": {
                 "body": {

data/spec/parslet_spec.rb

@@ -1,8 +1,13 @@
-require "pp"
 VERBOSE_MESSAGES = false
-require "spec_helper"
-require "#{Dir.pwd}/lib/oddb2xml/parslet_compositions"
+if File.exists?("#{Dir.pwd}/lib/oddb2xml/parslet_compositions.rb")
+  require_relative "../lib/oddb2xml/parslet_compositions"
+else
+  puts :ParseFailed
+  require_relative "../src/plugin/parslet_compositions"
+end
+
 require "parslet/rig/rspec"
+require "socket"
 
 hostname = Socket.gethostbyname(Socket.gethostname).first
 RUN_ALL_COMPOSITION_TESTS = false # /travis|localhost/i.match(hostname) != nil # takes about five minutes to run!
@@ -15,7 +20,6 @@ describe ParseComposition do
     string = "conserv.: E 216, E 218, excipiens pro suppositorio."
     composition = ParseComposition.from_string(string)
     # active_agent = ["hynic-[d-phe(1)", "tyr(3)-octeotridum]trifluoroacetum", "acidum ethylendiamini-n,n'-diaceticum"]
-
     active_substance = "HYNIC-[D-Phe(1)"
     composition_text = "II) Durchstechflasche 2: acidum ethylendiamini-N,N'-diaceticum 10 mg, dinatrii phosphas dodecahydricus, natrii hydroxidum, pro vitro."
     composition = ParseUtil.parse_compositions(composition_text, active_substance).first
@@ -1290,6 +1294,63 @@ describe ParseComposition do
     specify { expect(substance.unit).to eq nil }
   end
 
+  context "should handle 41174" do
+    string = "triamcinoloni acetonidum 10 mg, carmellosum natricum, natrii chloridum, polysorbatum 80, conserv.: alcohol benzylicus 9.9 mg, aqua ad iniectabile q.s. ad suspensionem pro 1 ml."
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.size).to be > 1 }
+    specify { expect(composition.substances.first.name).to eq "Triamcinoloni Acetonidum" }
+    specify { expect(composition.substances.last.name).to eq "Alcohol Benzylicus" }
+  end
+
+  context "should handle 67023" do
+    string = "noradrenalinum 0.06 mg ut noradrenalini tartras, natrii chloridum, acidum hydrochloridum, aqua ad iniectabile q.s. ad solutionem pro 1 ml corresp. natrium 3.308 mg."
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.size).to be > 1 }
+    specify { expect(composition.substances.first.name).to eq "Noradrenalinum" }
+    specify { expect(composition.substances.last.name).to eq "Acidum Hydrochloridum" }
+  end
+
+  context "should handle 67023" do
+    string = "noradrenalinum 0.06 mg ut noradrenalini tartras, natrii chloridum, acidum hydrochloridum, aqua ad iniectabile q.s. ad solutionem pro 1 ml corresp. natrium 3.308 mg."
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.size).to be > 0 }
+    specify { expect(composition.substances.first.name).to eq "Noradrenalinum" }
+    specify { expect(composition.substances.last.name).to eq "Acidum Hydrochloridum" }
+  end
+
+  context "should handle 67689" do
+    string = "daratumumabum 1800 mg, hyaluronidasum humanum ADNr, histidinum, histidini hydrochloridum monohydricum, sorbitolum 735.1 mg, methioninum, polysorbatum 20, aqua ad iniectabile ad solutionem pro 15 ml"
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.size).to be > 0 }
+    specify { expect(composition.substances.first.name).to eq "Daratumumabum" }
+    specify { expect(composition.substances.last.name).to eq "Polysorbatum 20" }
+  end
+
+  context "should handle 66097" do
+    string = "acidum acetylsalicylicum 100 mg, cellulosum microcristallinum, maydis amylum, silica colloidalis anhydrica, acidum stearicum, Überzug: acidi methacrylici et ethylis acrylatis polymerisatum 1:1, polysorbatum 80, natrii laurilsulfas corresp. natrium 2 µg, triethylis citras, talcum pro compresso obducto" # fails
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.first.name).to eq "Acidum Acetylsalicylicum" }
+    specify { expect(composition.substances.last.name).to eq "Talcum pro compresso Obducto" }
+  end
+  context "should handle 65828" do
+    string = " esomeprazolum 20 mg ut esomeprazolum magnesicum dihydricum, acidi methacrylici et ethylis acrylatis polymerisati 1:1 dispersio 30 per centum, natrii laurilsulfas, talcum, triethylis citras, hypromellosum, sacchari sphaerae corresp. saccharum 4.73 mg et maydis amylum, magnesii stearas, hydroxypropylcellulosum, glyceroli monostearas 40-55, polysorbatum 80, cellulosum microcristallinum, povidonum K 29-32, macrogolum 6000, crospovidonum, natrii stearylis fumaras, Überzug: hypromellosum, E 171, macrogolum 400, E 172 (rubrum), E 172 (flavum), pro compresso obducto corresp. natrium 0.01 mg."
+    composition = ParseComposition.from_string(string)
+    specify { expect(composition.source).to eq string }
+    specify { expect(composition.label).to eq nil }
+    specify { expect(composition.substances.first.name).to eq "Esomeprazolum" }
+    specify { expect(composition.substances.last.name).to eq "pro compresso Obducto" }
+  end
+
   context "should return correct composition for 'minoxidilum excipiens'" do
     string = "minoxidilum 2.5 mg, excipiens pro compresso."
     composition = ParseComposition.from_string(string)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: oddb2xml
 version: !ruby/object:Gem::Version
-  version: 2.7.4
+  version: 2.7.5
 platform: ruby
 authors:
 - Yasuhiro Asaka, Zeno R.R. Davatz, Niklaus Giger
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-30 00:00:00.000000000 Z
+date: 2022-02-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
@@ -70,16 +70,16 @@ dependencies:
   name: savon
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.12.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.12.0
 - !ruby/object:Gem::Dependency
   name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
@@ -336,16 +336,16 @@ dependencies:
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 6.3.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 6.3.3
 - !ruby/object:Gem::Dependency
   name: vcr
   requirement: !ruby/object:Gem::Requirement
@@ -388,6 +388,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: psych
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 4.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 4.0.0
 description: oddb2xml creates xml files using swissINDEX, BAG-XML and Swissmedic.
 email: yasaka@ywesee.com, zdavatz@ywesee.com, ngiger@ywesee.com
 executables:
@@ -439,6 +453,7 @@ files:
 - oddb2xml.gemspec
 - oddb2xml.xsd
 - oddb_calc.xsd
+- shell.nix
 - spec/artikelstamm_spec.rb
 - spec/builder_spec.rb
 - spec/calc_spec.rb
@@ -529,8 +544,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6.2
+rubygems_version: 3.3.3
 signing_key: 
 specification_version: 4
 summary: oddb2xml creates xml files.