ramaze.ch.oddb.org 1.0.0

data/README.txt

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+= ramaze.ch.oddb.org
+
+* http://scm.ywesee.com/?p=ch.oddb.org/.git;a=summary
+
+== DESCRIPTION:
+
+* ch.oddb.org running on Ramaze
+
+== FEATURES/PROBLEMS:
+
+* still a lot of missing Features from oddb.org
+
+== REQUIREMENTS:
+
+You need the following gems and Versions.
+
+  activesupport (2.3.2)
+  dbd-pg (0.3.9)
+  dbi (0.4.2)
+  deprecated (2.0.1)
+  facets (1.8.54)
+  gd2 (1.1.1)
+  haml (2.2.2)
+  innate (2010.07, 2009.10)
+  minitest (1.6.0)
+  pg (0.10.1, 0.8.0)
+  rack (1.2.1, 1.0.1)
+  ramaze (2009.10)
+  rdoc (2.5.9, 2.5.8)
+  rmagick (2.13.1)
+  turing (0.0.11)
+
+== INSTALL:
+
+* sudo gem install ramaze.ch.oddb.org
+
+== DEVELOPERS:
+
+* Zeno R.R. Davatz
+* Masaomi Hatakeyama
+* Hannes Wyss (upto Version 1.0)
+
+== LICENSE:
+
+* GPLv2.0

data/Rakefile

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+# -*- ruby -*-
+
+require 'rubygems'
+require 'hoe'
+
+# Hoe.plugin :compiler
+# Hoe.plugin :cucumberfeatures
+# Hoe.plugin :gem_prelude_sucks
+# Hoe.plugin :inline
+# Hoe.plugin :inline
+# Hoe.plugin :manifest
+# Hoe.plugin :newgem
+# Hoe.plugin :racc
+# Hoe.plugin :rubyforge
+# Hoe.plugin :rubyforge
+# Hoe.plugin :website
+
+Hoe.spec 'ramaze.ch.oddb.org' do
+  # HEY! If you fill these out in ~/.hoe_template/Rakefile.erb then
+  # you'll never have to touch them again!
+  # (delete this comment too, of course)
+
+developer('Masaomi Hatakeyama, Zeno R.R. Davatz', 'mhatakeyama@ywesee.com, zdavatz@ywesee.com')
+
+  # self.rubyforge_name = 'ramaze.ch.oddb.orgx' # if different than 'ramaze.ch.oddb.org'
+end
+
+# vim: syntax=ruby

data/bin/admin

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+#!/usr/bin/env ruby
+# Admin -- oddb -- 09.07.2003 -- hwyss@ywesee.com 
+
+$:.push(File.expand_path('../lib', File.dirname(__FILE__)))
+
+$KCODE = 'u'
+
+require 'drb'
+require 'sbsm/drb'
+require 'oddb'
+require 'oddb/config'
+require 'encoding/character/utf-8'
+require 'readline'
+include Readline
+
+Kernel.trap('INT') {
+  if($current.respond_to?(:exit))
+    $current.exit
+    $current = nil
+  else
+    puts "<ctrl-c> is used to kill admin-threads."
+    puts "Type <quit> or <exit> to exit."
+  end
+}
+
+prompt = 'de.oddb> '
+DRb.start_service('druby://localhost:0')
+oddb = DRbObject.new(nil, ODDB.config.server_url)
+last_error = nil
+priority = -1
+while(line = readline(prompt, true))
+  result = ''
+  result.extend(DRb::DRbUndumped)
+  line.strip!
+  $stdout.print "-> "
+  case line.downcase
+  when 'exit', 'quit'
+    $stdout.puts 'Goodbye'
+    break
+  when 'bt', 'backtrace'
+    if last_error.respond_to?(:backtrace)
+      $stdout.puts last_error.backtrace 
+    else
+      $stdout.puts 'No Error'
+    end
+  when /^last_error/
+    begin
+      $stdout.puts eval(line)
+    rescue Exception => last_error
+      $stdout.puts last_error
+    end
+  when /sp\s+(-?\d+)/, /set_priority\s+(-?\d+)/ 
+    priority = $~[1].to_i
+    $stdout.puts "setting Priority to #{priority}"
+  else
+    begin
+      bgflag = line.slice!(/\s*\&\s*$/)
+      $current = oddb._admin(line, result, priority)
+      unless(bgflag)
+        last_error = $current.join
+      end
+      $stdout.puts result
+    rescue Exception => last_error
+      $stdout.puts last_error
+    end
+  end
+  $current = nil
+  $stdout.flush
+end

data/bin/exportd

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+#!/usr/bin/env ruby
+
+$: << File.expand_path('../lib', File.dirname(__FILE__))
+$KCODE = 'u'
+
+require 'drb'
+require 'logger'
+require 'oddb/config'
+require 'oddb/drugs'
+require 'oddb/util'
+require 'oddb/export'
+require 'encoding/character/utf-8'
+
+module ODDB
+  require File.join('oddb', 'persistence', @config.persistence)
+  require File.join('oddb', 'persistence', @config.persistence, 'export')
+  persistence = nil
+  case @config.persistence
+  when 'odba'
+    DRb.install_id_conv ODBA::DRbIdConv.new
+    @persistence = ODDB::Persistence::ODBA
+  when 'og'
+    DRb.install_id_conv DRb::TimerIdConv.new
+    Og.setup({
+      :name     => @config.db_name,
+      :user     => @config.db_user,
+      :password => @config.db_auth,
+      :store    => @config.db_backend,
+      :evolve_schema => true,
+      :evolve_schema_cautious => false,
+    })
+    @persistence = ODDB::Persistence::Og
+  end
+
+  log_file = @config.log_file_export
+  if(log_file.is_a?(String))
+    FileUtils.mkdir_p(File.dirname(log_file))
+    log_file = File.open(log_file, 'a')
+    at_exit { log_file.close }
+  end
+  logger = Logger.new(log_file)
+  logger.level = Logger.const_get(@config.log_level_export)
+  @logger = logger
+
+  Currency = DRbObject.new(nil, @config.currency_rates)
+
+  begin
+    server = ODDB::Export::Server
+    server.extend(DRbUndumped)
+    @server = server
+
+    url = @config.server_url_export
+    url.untaint
+    DRb.start_service(url, server)
+    $SAFE = 1
+    logger.info('start') { 
+      sprintf("starting export-server on %s", url) }
+    DRb.thread.join
+  rescue Exception => error
+    logger.error('fatal') { error }
+    raise
+  end
+end

data/bin/migrate

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+#!/usr/bin/env ruby19
+
+$: << File.expand_path('../lib', File.dirname(__FILE__))
+
+require 'drb'
+require 'oddb/persistence/odba'
+require 'odba/18_19_loading_compatibility'
+
+$project_path, url, _ = ARGV
+$project_path ||= '/var/www/oddb.org'
+url ||= 'druby://localhost:10000'
+
+count = ODBA.cache.count(ODDB::Business::Company)
+unless count == 0
+  padding = " " * $0.length
+  puts <<-EOS
+#$0 should only be used to migrate to an empty database,
+#{padding} but I found #{count} instances of ODDB::Business::Company.
+#{padding} Please reconfigure and retry.
+  EOS
+  exit -1
+end
+
+require 'oddb/business/price'
+require 'oddb/drugs/active_agent'
+require 'oddb/drugs/composition'
+require 'oddb/drugs/ddd'
+require 'oddb/drugs/part'
+require 'oddb/remote/business/company'
+require 'oddb/text/chapter'
+require 'oddb/text/document'
+require 'oddb/text/paragraph'
+require 'oddb/text/picture'
+require 'oddb/util/feedback'
+
+module ODDB
+  ## PatinfoDocument needs to be defined, because it is not a Persistable
+  #  in the legacy code
+  class PatinfoDocument
+    CHAPTERS = [ :amzv, :company, :galenic_form, :effects, :purpose,
+      :amendments, :contra_indications, :precautions, :pregnancy, :usage,
+      :unwanted_effects, :general_advice, :other_advice, :composition,
+      :packages, :distribution, :fabrication, :date ]
+    attr_accessor :__drbref, *CHAPTERS
+    attr_reader :descriptions, :name
+    def chapter_names
+      CHAPTERS
+    end
+    def empty?
+      false
+    end
+  end
+  class PatinfoDocument2001 < PatinfoDocument
+  end
+  module Text
+    class Section
+      attr_reader :subheading, :paragraphs
+    end
+    class ImageLink
+      attr_reader :src
+    end
+    class Cell < Paragraph
+    end
+  end
+end
+
+DRb.start_service 'druby://localhost:0'
+
+server = DRb::DRbObject.new(nil, url)
+begin
+  server.admin "self.class"
+rescue DRb::DRbConnError
+  puts <<-EOS
+#$0 tried to import data from ch.oddb.org at #{url} but could not connect.
+Exiting.
+  EOS
+  exit -1
+end
+
+def longest_common_prefix names
+  if min = names.compact.collect do |name| name.length end.min
+    names.collect! do |name| name[0,min] end
+    first = names.first
+    until(names.all? do |name| name == first end) do
+      names.each do |name| name.chop! end
+    end
+    first
+  end
+end
+def migrate_active_agent composition, agent
+  substance = migrate_substance agent.substance
+  remote = agent.dose
+  dose = remote ? ODDB::Drugs::Dose.from_quanty(remote) : nil
+  created = ODDB::Drugs::ActiveAgent.new substance, dose
+    created.composition = composition
+    created.save
+end
+$atc_ptrn = %r{^[ABCDGHJLMNPRSV]([0-9]{2}([A-Z]([A-Z]([0-9]{2}))?)?)?$}
+def migrate_atc atc, sequence=nil
+                                 ## reject code B6
+  if atc && (code = atc.code) && $atc_ptrn.match(code)
+    code.force_encoding 'UTF-8'
+    created = ODDB::Drugs::Atc.find_by_code(code)
+    unless created
+      created = ODDB::Drugs::Atc.new code
+      migrate_multilingual atc, created.name
+      [:guidelines, :ddd_guidelines].each do |key|
+        if guidelines = atc.send(key)
+          created.send(key).en = guidelines.en.to_s
+          created.send(key).en.force_encoding 'UTF-8'
+        end
+      end
+      created.save
+      atc.remote.ddds.each_value do |ddd|
+        if dose = ddd.dose
+          roa = ddd.administration_route
+          roa.force_encoding 'UTF-8'
+          cddd = ODDB::Drugs::Ddd.new roa
+          cddd.dose = ddd.dose
+          if comment = ddd.note
+            comment.force_encoding 'UTF-8'
+            cddd.comment = comment
+          end
+          cddd.atc = created
+        end
+      end
+    end
+    sequence.atc = created if sequence
+  end
+rescue NoMethodError
+  puts atc.inspect
+  raise
+end
+def migrate_company company
+  created = ODDB::Business::Company.new
+  created.name.de = company.name.de
+  created.name.de.force_encoding 'UTF-8'
+  created.data_origins[:migration] = company.uid
+  created.save
+  company.products.each do |prod|
+    migrate_product prod, created
+  end
+end
+def migrate_composition sequence, composition
+  created = ODDB::Drugs::Composition.new
+  if galenic_form = composition.galenic_form
+    created.galenic_form = migrate_galenic_form galenic_form
+  end
+  composition.active_agents.each do |act|
+    migrate_active_agent created, act
+  end
+  created.sequence = sequence
+  created.save
+  nil ## prevent DRb::DRbConnError (too large packet)
+end
+def migrate_feedback item, feedback
+  created = ODDB::Util::Feedback.new
+  [:name, :email, :message, :time].each do |key|
+    value = feedback.send(key)
+    if value.is_a?(String)
+      value.force_encoding 'UTF-8'
+    end
+    created.send "#{key}=", value
+  end
+  created.email_public = feedback.show_email
+  created.item_good_experience = feedback.experience
+  created.item_recommended = feedback.recommend
+  created.item_good_impression = feedback.impression
+  created.item_helps = feedback.helps
+  created.item = item
+  created.save
+  nil ## prevent DRb::DRbConnError (too large packet)
+rescue NoMethodError
+  puts feedback.inspect
+end
+def migrate_galenic_form galenic_form
+  created = nil
+  galenic_form.all_descriptions.any? do |description|
+    description.force_encoding 'UTF-8'
+    created = ODDB::Drugs::GalenicForm.find_by_description description
+  end
+  unless created
+    created = ODDB::Drugs::GalenicForm.new
+    migrate_multilingual galenic_form, created.description
+    created.save
+  end
+  created
+end
+def migrate_m10l_document from, to
+  %w{de fr it en lt}.each do |key|
+    if (remote = from.descriptions[key]) && !remote.empty?
+      doc = ODDB::Text::Document.find_by_source remote.uid
+      unless doc
+        doc = ODDB::Text::Document.new
+        namechap = ODDB::Text::Chapter.new('name')
+        paragraph = ODDB::Text::Paragraph.new remote.name
+        namechap.add_paragraph paragraph
+        doc.add_chapter namechap
+        remote.chapter_names.each do |name|
+          begin
+            if name != :name && (rchap = remote.send(name))
+              ## update some chapter names
+              name = {
+                :contra_indications => 'counterindications',
+                :packages           => 'packaging',
+                :preclinic          => 'preclinicals',
+              }.fetch name, name.to_s
+              chapter = ODDB::Text::Chapter.new(name)
+              heading = if rchap.respond_to?(:heading)
+                          rchap.heading
+                        else
+                          rchap.instance_variable_get :@heading
+                        end
+              paragraph = ODDB::Text::Paragraph.new
+              paragraph.set_format 'b'
+              heading.force_encoding 'UTF-8'
+              paragraph << heading
+              chapter.add_paragraph paragraph
+              chapter.paragraphs.concat migrate_sections(rchap)
+              doc.add_chapter chapter
+            end
+          rescue TypeError
+            puts rchap.inspect
+            puts chapter.inspect
+            puts heading.inspect
+            raise
+          end
+        end
+        doc.source = remote.uid
+      end
+      to.send "#{key}=", doc
+      to.send(key).save
+      to.save
+    end
+  end
+  nil ## prevent DRb::DRbConnError (too large packet)
+rescue NoMethodError
+  puts from.inspect
+  puts from.descriptions.inspect
+  puts from.descriptions['de'].inspect
+  raise
+end
+def migrate_multilingual from, to
+  %w{de fr it en lt}.each do |key|
+    if desc = from.descriptions[key]
+      desc.force_encoding 'UTF-8'
+      to.send "#{key}=", desc
+    end
+    if to.respond_to?(:synonyms) && from.respond_to?(:synonyms)
+      to.synonyms.concat(from.synonyms.uniq - to.all)
+      to.synonyms.each do |syn| syn.force_encoding 'UTF-8' end
+    end
+  end
+  to
+end
+def migrate_package sequence, package
+  created = ODDB::Drugs::Package.new
+  created.name.de = sequence.name.de
+  created.add_code ODDB::Util::Code.new(:cid, package.ikskey, 'CH')
+  if pcode = package.pharmacode
+    created.add_code ODDB::Util::Code.new(:pharmacode, pcode, 'CH')
+  end
+  package.prices.each do |key, prices|
+    unless prices.empty?
+      price = ODDB::Business::Price.new key, 'CH'
+      prices.each do |remote|
+        price.value = remote.to_f, remote.valid_from
+      end
+      created.add_price price
+    end
+  end
+  package.parts.each_with_index do |part, idx|
+    migrate_part created, part, sequence, idx
+  end
+  package.feedbacks.each do |feedback|
+    migrate_feedback created, feedback
+  end
+  created.sequence = sequence
+  nil ## prevent DRb::DRbConnError (too large packet)
+end
+def migrate_paragraph par
+  sanitized = ODDB::Text::Paragraph.new
+  par.text.force_encoding 'UTF-8'
+  sanitized << par.text
+  par.formats.each do |fmt|
+    fmt.values.collect! do |val|
+      {
+        :bold => 'b',
+        :italic => 'i',
+      }.fetch val, val.to_s
+    end
+  end
+  sanitized.formats.replace par.formats
+  sanitized
+end
+def migrate_part package, part, sequence, idx
+  created = ODDB::Drugs::Part.new
+  created.multi = part.multi
+  created.size = part.size
+  created.quantity = part.measure
+  if remote = part.remote.commercial_form
+    unit = nil
+    remote.all_descriptions.any? do |name|
+      unit = ODDB::Drugs::Unit.find_by_name
+    end
+    unless unit
+      unit = ODDB::Drugs::Unit.new
+      migrate_multilingual remote, unit.name
+    end
+    created.unit = unit
+  end
+  created.composition = sequence.compositions[idx] || sequence.compositions.last
+  created.package = package
+  created.save
+  nil ## prevent DRb::DRbConnError (too large packet)
+end
+def migrate_product product, company
+  names = product.sequences.collect do |seq|
+    name = seq.name_base[/^(.(?!,?[ \-]\d))+(.|$)/] || seq.name_base.to_s
+    name.force_encoding 'UTF-8'
+    name
+  end
+  name = nil
+  created = nil
+  if prefix = longest_common_prefix(names)
+    postfix = company.name.de[/(.{4}[^ ]+)|(^.{1,4}$)/]
+    name = prefix.include?(postfix) ? prefix : sprintf("%s %s", prefix, postfix)
+    created = ODDB::Drugs::Product.find_by_name name
+    if created && created.company != company
+      warn sprintf("%s and %s both have a Product called '%s'",
+                    company.name.de, created.company.name.de, name)
+      created = company.products.find do |prod| prod.name.de == name end
+    end
+  end
+  created ||= ODDB::Drugs::Product.new
+  if name
+    created.name.de = name
+    created.name.de.force_encoding 'UTF-8'
+  end
+  created.company = company
+  created.save
+  registration = ODDB::Regulatory::Registration.new
+  registration.code = product.iksnr
+  registration.registration_date = product.registration_date
+  registration.revision_date = product.revision_date
+  registration.expiration_date = product.expiration_date
+  registration.deactivation_date = product.inactive_date
+  swissmedic = ODDB::Regulatory::Authority.find_by_name('Swissmedic') or begin
+    swissmedic = ODDB::Regulatory::Authority.new
+    swissmedic.name.de = 'Swissmedic'
+    swissmedic.url = 'http://www.swissmedic.ch'
+    swissmedic.save
+  end
+  registration.authority = swissmedic
+  product.sequences.each do |seq| 
+    migrate_sequence created, registration, seq
+  end
+  nil ## prevent DRb::DRbConnError (too large packet)
+end
+def migrate_sections chapter
+  sections = if chapter.respond_to?(:sections)
+               chapter.sections
+             else
+               chapter.instance_variable_get :@sections
+             end
+  paragraphs = []
+  sections.each do |section|
+    if (subh = section.subheading) && !subh.empty?
+      paragraph = ODDB::Text::Paragraph.new
+      paragraph.set_format 'i'
+      subh.force_encoding 'UTF-8'
+      paragraph << subh
+      paragraphs.push paragraph
+    end
+    section.paragraphs.each do |par|
+      case par
+      when ODDB::Text::ImageLink
+        path = File.join $project_path, 'doc', par.src
+        if File.exist?(path)
+          pic = ODDB::Text::Picture.new
+          data = File.open(path, 'rb') do |fh| fh.read end
+          pic.replace data.unpack('H*').first
+          img = pic.image
+          pic.height = img.rows
+          pic.width = img.columns
+          paragraphs.push pic
+        end
+      when ODDB::Text::Table
+        par.rows.each do |row|
+          row.collect! do |cell|
+            migrate_paragraph(cell)
+          end
+        end
+        paragraphs.push par
+      else
+        paragraphs.push migrate_paragraph(par)
+      end
+    end
+  end
+  paragraphs
+rescue NoMethodError
+  puts chapter.inspect, sections.inspect
+  raise
+end
+def migrate_sequence product, registration, sequence
+  created = ODDB::Drugs::Sequence.new
+  basename = sequence.name_base
+  basename.force_encoding 'UTF-8'
+  created.name.de = basename
+  migrate_atc sequence.atc, created
+  sequence.compositions.each do |comp|
+    migrate_composition created, comp
+  end
+  sequence.packages.each do |pac|
+    migrate_package created, pac
+  end
+  [:fachinfo, :patinfo].each do |key|
+    if info = sequence.send(key)
+      migrate_m10l_document info, created.send(key)
+    end
+  end
+  created.product = product
+  created.save
+  nil ## prevent DRb::DRbConnError (too large packet)
+rescue DRb::DRbConnError
+  puts sequence.inspect
+  puts sequence.compositions.inspect
+end
+def migrate_substance substance
+  created = nil
+  substance.all_descriptions.any? do |description|
+    description.force_encoding 'UTF-8'
+    created = ODDB::Drugs::Substance.find_by_name description
+  end
+  unless created
+    created = ODDB::Drugs::Substance.new
+    migrate_multilingual substance, created.name
+    created.save
+  end
+  created
+end
+
+total = server.company_count.to_f
+count = 0
+server.remote_each_atc_class do |atc|
+  unless atc.en.to_s.empty?
+    migrate_atc ODDB::Remote::Drugs::Atc.new url, atc
+  end
+end
+server.remote_each_company do |remote|
+  company = ODDB::Remote::Business::Company.new(url, remote)
+  unless company.products.empty?
+    migrate_company company
+  end
+  count += 1
+  print (" " * 8) \
+    << ("\b" * 8) \
+    << sprintf('%7.3f%%', count*100/total) \
+    << ("\b" * 8)
+  $stdout.flush
+end