oddb2xml 2.6.8 → 2.6.9

checksums.yaml

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

@@ -1,3 +1,8 @@
+=== 2.6.9 / 29.06.2020
+
+* Fix problem when running bin/oddb2xml -a -f dat. Thanks to Lukas Furre for reporting the problem
+* Fix warning with regular expression thas has ']'
+
 === 2.6.8 / 26.06.2020
 
 * Re-Add support for Ruby Version 2.4

data/lib/oddb2xml/builder.rb

@@ -1337,7 +1337,7 @@ module Oddb2xml
                                           else
                                             ('0' * DAT_LEN[:ITHE])
                                           end.to_i
-          row << "%0#{DAT_LEN[:CEAN]}d" % (sprintf('%013d', ean).match(/^000000/) ? 0 : ean.to_i)
+          row << "%0#{DAT_LEN[:CEAN]}d" % (sprintf('%013d', ean.to_i).match(/^000000/) ? 0 : ean.to_i)
           row << "%#{DAT_LEN[:CMWS]}s"  % '2' # pharma
           rows << row
       end

data/lib/oddb2xml/cli.rb

@@ -157,7 +157,9 @@ module Oddb2xml
             end
           end
           if @options[:calc]
-            FileUtils.cp(File.join(WorkDir, file), File.join(WorkDir, file.sub('.xml', '_'+Time.now.strftime("%d.%m.%Y_%H.%M")+'.xml')), :verbose => false)
+            ext = File.extname(file)
+            dest = File.join(WorkDir, file.sub(ext, '_'+Time.now.strftime("%d.%m.%Y_%H.%M")+ext))
+            FileUtils.cp(File.join(WorkDir, file), dest, :verbose => false)
           end
         end
       rescue Interrupt

data/lib/oddb2xml/parslet_compositions.rb

@@ -88,7 +88,11 @@ module ParseUtil
         composition.substances.each do
           |substance_item|
           active_substance_name = substance_item.name.downcase.sub(/^cum\s/, '')
-          substance_item.is_active_agent = (active_agents.find {|x| /#{x.downcase.gsub('(', '\(').gsub(')', '\)')}($|\s)/.match(active_substance_name) } != nil)
+          substance_item.is_active_agent = (active_agents.find {|x| /#{x.downcase.
+                                                                gsub('(', '\(').
+                                                                gsub(')', '\)').
+                                                                gsub('[', '\[').
+                                                                gsub(']', '\]')}($|\s)/.match(active_substance_name) } != nil)
           substance_item.is_active_agent = true if substance_item.chemical_substance and active_agents.find {|x| x.downcase.eql?(substance_item.chemical_substance.name.downcase) }
          end
         comps << composition

data/lib/oddb2xml/util.rb

@@ -69,7 +69,7 @@ module Oddb2xml
   def Oddb2xml.add_epha_changes_for_ATC(iksnr, atc_code, force_run: false)
     @atc_csv_content  =  {} if force_run
     if @atc_csv_content.size == 0
-      open(@atc_csv_origin).readlines.each{
+      Oddb2xml.uri_open(@atc_csv_origin).readlines.each{
         |line|
           items = line.split(',')
           @atc_csv_content[[items[0], items[1]]] = items[2]

data/lib/oddb2xml/version.rb

@@ -1,3 +1,3 @@
 module Oddb2xml
-  VERSION = "2.6.8"
+  VERSION = "2.6.9"
 end

data/spec/cli_spec.rb

@@ -184,6 +184,32 @@ describe Oddb2xml::Cli do
             }
     end
   end
+  context 'when  -e and -f dat option is given' do
+    before(:all) do
+      cleanup_directories_before_run
+      options = Oddb2xml::Options.parse('-e -f dat')
+      @cli = Oddb2xml::Cli.new(options)
+      @cli_output = buildr_capture(:stdout) { @cli.run }
+    end
+    it_behaves_like 'any interface for product'
+    it 'should have calc option' do
+      expect(@cli).to have_option(:format => :dat)
+      expect(@cli).to have_option(:calc => true)
+      expect(@cli).to have_option(:extended => true)
+    end
+    it 'should create xml files' do
+      expect(@cli_output).to match(/NonPharma/)
+      file_today = "oddb_calc_#{Time.now.strftime("%d.%m.%Y_%H.%M")}.xml"
+      expect(Dir.glob(File.join(Oddb2xml::WorkDir, 'oddb_calc.xml')).size).to eq 1
+      expect(Dir.glob(File.join(Oddb2xml::WorkDir, file_today)).size).to eq 1
+    end
+    it 'should create migel files' do
+      expect(@cli_output).to match(/NonPharma/)
+      file_today = "oddb_with_migel_#{Time.now.strftime("%d.%m.%Y_%H.%M")}.dat"
+      expect(Dir.glob(File.join(Oddb2xml::WorkDir, 'oddb_with_migel.dat')).size).to eq 1
+      expect(Dir.glob(File.join(Oddb2xml::WorkDir, file_today)).size).to eq 1
+    end
+  end
 
   context 'when -a nonpharma option is given' do
     before(:all) do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: oddb2xml
 version: !ruby/object:Gem::Version
-  version: 2.6.8
+  version: 2.6.9
 platform: ruby
 authors:
 - Yasuhiro Asaka, Zeno R.R. Davatz, Niklaus Giger
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-06-26 00:00:00.000000000 Z
+date: 2020-06-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
@@ -486,7 +486,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubyforge_project: 
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: oddb2xml creates xml files.