Merge pull request #255 from ngiger/master

src/plugin/text_info.rb

@@ -56,7 +56,6 @@ def initialize app, opts={:newest => true}
       @wrong_meta_tags = []
       @news_log = File.join ODDB.config.log_dir, 'textinfos.txt'
       @problematic_fi_pi = File.join ODDB.config.log_dir, 'problematic_fi_pi.lst'
-      @missing_override_file = File.join ODDB.config.log_dir, 'missing_override.lst'
       @title  = ''       # target fi/pi name
       @format = :swissmedicinfo
       @target = :both
@@ -73,8 +72,9 @@ def initialize app, opts={:newest => true}
       @fi_atc_code_missmatch = []
       @target_keys = Util::COLUMNS_FEBRUARY_2019
       @iksnrs_meta_info = {}
+      @specify_barcode_to_text_info ||= {}
       @skipped_override ||= []
-      @missing_override ||= []
+      @missing_override ||= {}
     end
     def save_info type, name, lang, page, flags={}
       dir = File.join @dirs[type], lang.to_s
@@ -405,7 +405,7 @@ def update_patinfo_lang(meta_info, pis)
                   @skipped_override << barcode_override
                 else
                   LogFile.debug "missing_override: not found via #{barcode_override}: '#{name}' != '#{meta_info.title}'"
-                  @missing_override << "#{barcode_override}: #{meta_info.title} # != override #{name}"
+                  @missing_override["#{barcode_override}"] = "#{meta_info.title} # != override #{name}"
                 end
                 puts "package.patinfo updated sequence #{package.iksnr}/#{package.seqnr}/#{package.ikscd} #{package.pointer}"
               end
@@ -603,6 +603,7 @@ def report
         res << "\n#{Override_file}: The #{@missing_override.size} missing overrides are\n"
         res << @missing_override.join("\n")
       end
+      File.open(Override_file, 'w+' ) { |out| YAML.dump(@specify_barcode_to_text_info.merge(@missing_override), out,  line_width: -1 )}
       res
     end
     def init_agent
@@ -647,7 +648,7 @@ def TextInfoPlugin::create_sequence(app, registration, title, seqNr ='00', packN
       # are found after an import_daily
       registration.sequences.values.first.name_base = title;
       registration.sequences.values.first.odba_store;
-      LogFile.debug "create_sequence #{registration.iksnr} seqNr #{seqNr}  #{sequence.pointer} seq_args #{seq_args} app.name #{title} should match #{app.registration(registration.iksnr).name_base} registration.sequences #{registration.sequences}"
+      LogFile.debug "create_sequence #{registration.iksnr} seqNr #{seqNr}  #{sequence.pointer} seq_args #{seq_args.keys} app.name #{title} should match #{app.registration(registration.iksnr).name_base} registration.sequences #{registration.sequences}"
     end
 
     def TextInfoPlugin::create_registration(app, info, seqNr ='00', packNr = '000')
@@ -1367,7 +1368,6 @@ def handle_chunk(chunk)
     def report_problematic_names
       LogFile.debug "Creating #{@problematic_fi_pi} with #{@duplicate_entries.size} @duplicate_entries"
       File.open(@problematic_fi_pi, 'w+') do |file|
-        file.write("# resolve these problems and add them to #{@missing_override_file}")
         @iksnrs_from_aips.sort.uniq.each do|iksnr|
           file.puts "# known packages. There are #{@duplicate_entries.size} @duplicate_entries"
           @app.registration(iksnr).packages.each do |pack|
@@ -1509,7 +1509,6 @@ def import_swissmedicinfo(options=nil)
       @iksnrs_meta_info.values.flatten.sort{|x,y| x.iksnr.to_i <=> y.iksnr.to_i}.each do |meta_info|
         parse_textinfo(meta_info)
       end
-      File.open(@missing_override_file, 'w+') {|f| f.puts  @missing_override.join("\n")}
       if @options[:download] != false
         puts_sync "job is done. now postprocess works ..."
         postprocess

test/test_plugin/swissmedic.rb

@@ -71,13 +71,13 @@ def setup
       prep_from = File.expand_path('../data/xlsx/Erweiterte_Arzneimittelliste_HAM_31012019.xlsx', File.dirname(__FILE__))
       @plugin.should_receive(:fetch_with_http).with( ODDB::SwissmedicPlugin.get_packages_url).and_return(File.open(@state_2015_07_02).read).by_default
       @plugin.should_receive(:fetch_with_http).with( ODDB::SwissmedicPlugin.get_preparations_url).and_return(File.open(prep_from).read).by_default
-      @target   = File.join @archive, 'xls',  @@today.strftime('Packungen-%Y.%m.%d.xlsx')
-      @latest   = File.join @archive, 'xls', 'Packungen-latest.xlsx'
+      @target = File.join @archive, 'xls',  @@today.strftime('Packungen-%Y.%m.%d.xlsx')
+      @latest = File.join @archive, 'xls', 'Packungen-latest.xlsx'
       FileUtils.makedirs(File.dirname(@latest)) unless File.exist?(File.dirname(@latest))
       FileUtils.rm(@latest) if File.exist?(@latest)
 
-      @test_packages = File.expand_path '../data/xlsx/Packungen-2019.01.31.xlsx', File.dirname(__FILE__)
-      latest_to = File.expand_path('../../data/xls/Packungen-latest.xlsx', File.dirname(__FILE__))
+      @test_packages = File.expand_path('../data/xlsx/Packungen-2019.01.31.xlsx', File.dirname(__FILE__))
+      latest_to =      File.expand_path('../data/xls/Packungen-latest.xlsx', File.dirname(__FILE__))
       FileUtils.makedirs(File.dirname(latest_to))
       FileUtils.cp(@test_packages, latest_to, :verbose => true, :preserve => true)
       FileUtils.cp(prep_from, File.join(@archive, 'xls',  @@today.strftime('Präparateliste-%Y.%m.%d.xlsx')),

test/test_plugin/text_info.rb

@@ -12,7 +12,6 @@
 require 'plugin/text_info'
 require 'model/text'
 module ODDB
-  RUN_ALL = false
   class FachinfoDocument
 		def odba_id
 			1
@@ -160,7 +159,7 @@ def test_true_news
       old_news = ["Amiodarone Winthrop\302\256/- Mite"]
       assert_equal news, @plugin.true_news(news, old_news)
     end
-  end if RUN_ALL
+  end
 
   class TestExtractMatchedName <MiniTest::Test
     Nr_FI_in_AIPS_test = 4
@@ -171,15 +170,19 @@ def teardown
     end
 
     def setup
+      path_check = File.expand_path(File.join(File.dirname(__FILE__),  '../../etc', 'barcode_minitest.yml'))
+      assert_equal(ODDB::TextInfoPlugin::Override_file, path_check)
+      FileUtils.rm_f(path_check, :verbose => true)
       pointer = flexmock 'pointer'
       @aips_download = File.expand_path('../data/xml/Aips_test.xml', File.dirname(__FILE__))
       latest_from = File.expand_path('../data/xlsx/Packungen-latest.xlsx', File.dirname(__FILE__))
       latest_to = File.expand_path('../../data/xls/Packungen-latest.xlsx', File.dirname(__FILE__))
       FileUtils.cp(latest_from, latest_to, :verbose => true, :preserve => true)
       @app = flexmock 'application'
-      @reg = flexmock 'registration'
+      @reg = flexmock "registration_#{__LINE__}"
       @reg.should_receive(:pointer).and_return(pointer).by_default
       @reg.should_receive(:odba_store).and_return(nil).by_default
+      @reg.should_receive(:odba_isolated_store).and_return(nil).by_default
       @reg.should_receive(:company).and_return('company')
       @reg.should_receive(:inactive?).and_return(false)
       lang_de = flexmock 'lang_de'
@@ -204,21 +207,27 @@ def setup
 
       @app.should_receive(:create_patinfo).and_return(Patinfo.new)
 
-      atc_class = flexmock('atc_class')
+      atc_class = flexmock("atc_class_#{__LINE__}")
+      atc_class.should_receive(:oid).and_return('oid')
       atc_class.should_receive(:code).and_return('code')
-      @sequence = flexmock 'sequence'
+      @sequence = flexmock "sequence_#{__LINE__}"
       @sequence.should_receive(:seqnr).and_return('01')
       @sequence.should_receive(:pointer).and_return(pointer)
       @sequence.should_receive(:odb_store)
+      @sequence.should_receive(:odba_isolated_store)
+      @sequence.should_receive(:atc_class=).and_return(atc_class)
       @sequence.should_receive(:atc_class).and_return(atc_class)
       @sequence.should_receive(:patinfo).and_return(nil).by_default
       @sequence.should_receive(:patinfo=).and_return(nil).by_default
       @sequence.should_receive(:odba_store)
       @package = flexmock('package')
       @sequence.should_receive(:package).and_return(@package)
 
-      atc_class = flexmock 'atc_class'
+      atc_class = flexmock("atc_class_#{__LINE__}")
+      atc_class.should_receive(:oid).and_return('oid')
+      atc_class.should_receive(:code).and_return('code')
       atc_class.should_receive(:pointer).and_return(pointer)
+      atc_class.should_receive(:odba_store).and_return(true)
       @app.should_receive(:atc_class).and_return(atc_class)
       @app.should_receive(:update).and_return(@fachinfo)
       @reg.should_receive(:fachinfo).and_return(@fachinfo)
@@ -245,7 +254,7 @@ def setup
                   :xml_file => @aips_download,
                   }
     end
-if RUN_ALL
+
     def test_53662_pi_de
       @options[:iksnrs] = ['53662']
       @plugin.import_swissmedicinfo(@options)
@@ -281,15 +290,15 @@ def test_import_daily_fi
 
       assert_equal(Nr_PI_in_AIPS_test, @plugin.iksnrs_meta_info.keys.find_all{|key| key[1] == 'pi'}.size, 'must find patinfo')
 
-      assert_equal(Nr_PI_in_AIPS_test, @plugin.updated_fis.size, 'nr updated fis must match')
+      assert_equal(Nr_FI_in_AIPS_test, @plugin.updated_fis.size, 'nr updated fis must match')
       assert_equal(0, @plugin.updated_pis.size, 'nr updated pis must match')
 
       assert_equal(0, @plugin.corrected_fis.size, 'corrected_fis must match')
       assert_equal(0, @plugin.corrected_pis.size, 'corrected_pis must match')
 
       assert_equal(0, @plugin.up_to_date_pis, 'up_to_date_pis must match')
       # nr_fis = 6 # we add all missing
-      assert_equal(3, @plugin.up_to_date_fis, 'up_to_date_fis must match')
+      assert_equal(0, @plugin.up_to_date_fis, 'up_to_date_fis must match')
 
       @plugin = TextInfoPlugin.new @app
       @plugin.parser = @parser
@@ -319,20 +328,32 @@ def test_import_daily_pi
       assert_equal(0, @plugin.updated_fis.size, 'nr updated fis must match')
       assert_equal(0, @plugin.up_to_date_fis, 'up_to_date_fis must match')
     end
-  end
     def test_import_daily_packungen
       @options[:target] = :pi
       @options[:newest] = true
+      old_missing = {'680109990223_pi_de' =>  'Osanit® Kügelchen',
+                     '7680109990223_pi_fr' => 'Osanit® globules',
+                     '7680109990224_pi_fr' => 'Test mit langem Namen der nicht umgebrochen sein sollte mehr als 80 Zeichen lang'}
+      real_override_file = File.join(File.dirname(__FILE__),  '../../etc', 'barcode_to_text_info.yml')
+      assert_equal(false, File.exist?(ODDB::TextInfoPlugin::Override_file), "File #{ODDB::TextInfoPlugin::Override_file} must not exist")
+      assert_equal(true, File.exist?(real_override_file), "File #{real_override_file} must exist")
+      real_overrides = YAML.load(File.read(real_override_file))
+      File.open(ODDB::TextInfoPlugin::Override_file, 'w+' ) do |out|
+        YAML.dump(old_missing, out)
+      end
+      assert_equal(5, File.readlines(ODDB::TextInfoPlugin::Override_file).size, 'File must be now 5 lines long, as one is too long')
+      old_time = File.ctime(ODDB::TextInfoPlugin::Override_file)
       # Add tests that patinfo gets updated
       @plugin.import_swissmedicinfo(@options)
-
       puts @plugin.report
       assert(@plugin.iksnrs_meta_info.keys.find_all{|key| key[1] == 'pi'}.size > 0, 'must find at least one find patinfo')
       assert_equal(Nr_FI_in_AIPS_test, @plugin.iksnrs_meta_info.keys.find_all{|key| key[1] == 'fi'}.size, 'must find fachinfo')
       assert_equal(Nr_PI_in_AIPS_test, @plugin.iksnrs_meta_info.keys.find_all{|key| key[1] == 'pi'}.size, 'may not find patinfo')
       assert_equal(Nr_PI_in_AIPS_test , @plugin.updated_pis.size, 'nr updated pis must match')
       assert_equal(Nr_PI_in_AIPS_test, @plugin.corrected_pis.size, "nr corrected_pis must match")
-
+      new_time = File.ctime(ODDB::TextInfoPlugin::Override_file)
+      assert(new_time > old_time, "ctime of #{ODDB::TextInfoPlugin::Override_file} should have changed")
+      assert_equal(4, File.readlines(ODDB::TextInfoPlugin::Override_file).size, 'File must be now 4 lines long')
       assert_equal(0, @plugin.corrected_fis.size, 'nr corrected_fis must match')
       assert_equal(0, @plugin.updated_fis.size, 'nr updated fis must match')
       assert_equal(0, @plugin.up_to_date_fis, 'up_to_date_fis must match')

test/test_plugin/text_info_swissmedicinfo.rb

@@ -488,10 +488,9 @@ def test_import_patinfo_tramal_43788
       replace_constant('ODDB::RefdataPlugin::REFDATA_SERVER', @server) do
         assert(@plugin.import_swissmedicinfo(@opts), 'must be able to run import_swissmedicinfo')
       end
-      [ @plugin.problematic_fi_pi, @plugin.missing_override_file].each do |filename|
-        assert(File.exist?(filename))
-        # assert(File.size(filename) > 100, "#{filename} must be longer than 100 chars, but is only #{File.size(filename)}")
-      end
+      assert(File.exist?(@plugin.problematic_fi_pi), "Datei #{ @plugin.problematic_fi_pi} must exist")
+      path = File.join(File.dirname(__FILE__), '../../doc/resources/images/pi/de/43788Tramal_Tropfen__L_sung_zum_Einnehmen_files/1.png')
+      assert(File.exist?(path), "Created image file #{path} must exist")
       @app.registration('15219').packages.size
       @app.registration('15219').packages.values.find_all { |x| x.patinfo}
       @app.registration('15219').sequences.values.find_all { |x| x.patinfo}