Module: SwissmedicDiff::Diff

Included in:
SwissmedicDiff
Defined in:
lib/swissmedic-diff.rb

Constant Summary collapse

COLUMNS_2014 = 
{
    :iksnr => /Zulassungs-Nummer/i,                # column-nr: 0
    :seqnr => /Dosistärke-nummer|^Sequenz$/i,
    :name_base => /Präparatebezeichnung|^Sequenzname$/i,
    :company => /Zulassungsinhaberin/i,
    :index_therapeuticus => /IT-Nummer/i,
    :atc_class => /ATC-Code/i,                     # column-nr: 5
    :production_science => /Heilmittelcode/i,
    :registration_date => /Erstzul.datum Präp./i,
    :sequence_date => /Zul.datum Dosisstärke *|Zul.datum Sequenz/i,
    :expiry_date => /Gültigkeits-datum */i,
    :ikscd => /Verpackungs ID/i,                   # column-nr: 10
    :size => /Packungsgrösse/i,
    :unit => /Einheit/i,
    :ikscat => /Abgabekategorie/i,
    :substances => /Wirkstoff/i,
    :composition => /Zusammensetzung/i,             # column-nr: 15
    :indication_registration => /Anwendungsgebiet Präparate/i,
    :indication_sequence => /Anwendungsgebiet Dosisstärke|Anwendungsgebiet Sequenz/i,
}
COLUMNS_OLD = 
[ :iksnr, :seqnr, :name_base, :company,
:index_therapeuticus, :atc_class, :production_science,
:registration_date, :sequence_date, :expiry_date, :ikscd,
:size, :unit, :ikscat, :substances, :composition,
:indication_registration, :indication_sequence ]
COLUMNS_JULY_2015 = 
{
    :iksnr => /Zulassungs-Nummer/i,                  # column-nr: 0
    :seqnr => /Dosis+tärke-nummer/i,
    :name_base => /Präparatebezeichnung/i,
    :company => /Zulassungsinhaberin/i,
    :production_science => /Heilmittelcode/i,
    :index_therapeuticus => /IT-Nummer/i,            # column-nr: 5
    :atc_class => /ATC-Code/i,
    :registration_date => /Erstzulassungs-datum./i,
    :sequence_date => /Zul.datum Dosisstärke/i,
    :expiry_date => /Gültigkeitsdauer der Zulassung/i,
    :ikscd => /Packungscode/i,                 # column-nr: 10
    :size => /Packungsgrösse/i,
    :unit => /Einheit/i,
    :ikscat => /Abgabekategorie Packung/i,
    :ikscat_seq => /Abgabekategorie Dosisstärke/i,
    :ikscat_preparation => /Abgabekategorie Präparat/i, # column-nr: 15
    :substances => /Wirkstoff/i,
    :composition => /Zusammensetzung/i,
    :indication_registration => /Anwendungsgebiet Präparat/i,
    :indication_sequence => /Anwendungsgebiet Dosisstärke/i,
    :gen_production => /Gentechnisch hergestellte Wirkstoffe/i, # column-nr 20
    :insulin_category => /Kategorie bei Insulinen/i,
  # swissmedi corrected in february 2018 the typo  betäubunsmittel to  betäubungsmittel-
    :drug_index       => /Verz. bei betäubun.*smittel-haltigen Präparaten/i,
}
COLUMNS_FEBRUARY_2019 = 
{
  :iksnr => /Zulassungs-Nummer/i,                  # column-nr: 0
  :seqnr => /Dosisstärke-nummer/i,
  :name_base => /Bezeichnung des Arzneimittels/i,
  :company => /Zulassungsinhaberin/i,
  :production_science => /Heilmittelcode/i,
  :index_therapeuticus => /IT-Nummer/i,            # column-nr: 5
  :atc_class => /ATC-Code/i,
  :registration_date => /Erstzul.datum Arzneimittel/i,
  :sequence_date => /Zul.datum Dosisstärke/i,
  :expiry_date => /Gültigkeitsdauer der Zulassung/i,
  :ikscd => /Packungscode/i,                 # column-nr: 10
  :size => /Packungsgrösse/i,
  :unit => /Einheit/i,
  :ikscat => /Abgabekategorie Packung/i,
  :ikscat_seq => /Abgabekategorie Dosisstärke/i,
  :ikscat_preparation => /Abgabekategorie Arzneimittel/i, # column-nr: 15
  :substances => /Wirkstoff/i,
  :composition => /Zusammensetzung/i,
  :composition_AMZV => /Volldeklaration rev. AMZV umgesetzt/i,
  :indication_registration => /Anwendungsgebiet Arzneimittel/i,
  :indication_sequence => /Anwendungsgebiet Dosisstärke/i, # column-nr 20
  :gen_production => /Gentechnisch hergestellte Wirkstoffe/i,
  :insulin_category => /Kategorie bei Insulinen/i,
  # swissmedi corrected in february 2018 the typo  betäubunsmittel to  betäubungsmittel-
    :drug_index       => /Verz. bei betäubungsmittel-haltigen Arzneimittel/i,
}
FLAGS = 
{
  :new                      =>  'Neues Produkt',
  :name_base                =>  'Namensänderung',
  :ikscat                   =>  'Abgabekategorie',
  :index_therapeuticus      =>  'Index Therapeuticus',
  :indication_registration  =>  'Anwendungsgebiet Präparate',
  :indication_sequence      =>  'Anwendungsgebiet Sequenz',
  :company                  =>  'Zulassungsinhaber',
  :composition              =>  'Zusammensetzung',
  :sequence                 =>  'Packungen',
  :size                     =>  'Packungsgrösse',
  :expiry_date              =>  'Ablaufdatum der Zulassung',
  :registration_date        =>  'Erstzulassungsdatum',
  :sequence_date            =>  'Zulassungsdatum Sequenz',
  :delete                   =>  'Das Produkt wurde gelöscht',
  :replaced_package         =>  'Packungs-Nummer',
  :substances               =>  'Wirkstoffe',
  :production_science       =>  'Heilmittelcode',
  :atc_class                =>  'ATC-Code',
}
GALFORM_P = 
%r{excipiens\s+(ad|pro)\s+(?<galform>((?!\bpro\b)[^.])+)}
DATE_FORMAT = 
'%Y:%m:%d'

Instance Method Summary collapse

Instance Method Details

#_comparable(key, row, idx) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 356

def _comparable(key, row, idx)
  if cell = row[idx]
    case key
    when :registration_date, :expiry_date
      if  row[idx] && row[idx].value && REGEXP_UNLIMITED.match(row[idx].value.to_s)
        VALUE_UNLIMITED # Date.new(2099,12,31)
      else
        row[idx] && row[idx].value ? row[idx].value.to_date : nil
      end
    when :seqnr
      sprintf "%02i", cell(row, idx).to_i
    else
      cell(row, idx).downcase.gsub(/\s+/, "")
    end
  end
end

#_known_data(latest, known_regs, known_seqs, known_pacs, newest_rows) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 263

def _known_data(latest, known_regs, known_seqs, known_pacs, newest_rows)
  lbook = Spreadsheet.open(latest)
  @latest_keys = get_column_indices(lbook).keys
  idx, prr, prp = nil
  multiples = {}
  each_valid_row(lbook) { |row|
    iksnr = cell(row, @latest_keys.index(:iksnr))
    seqnr = cell(row, @latest_keys.index(:seqnr))
    pacnr = cell(row, @latest_keys.index(:ikscd))
    multiples[iksnr] ||= {}
    if prr == iksnr && prp == pacnr
      idx += 1
    elsif previous = multiples[iksnr][pacnr]
      prr = iksnr
      prp = pacnr
      idx = previous[@latest_keys.size].to_i + 1
    else
      prr = iksnr
      prp = pacnr
      idx = 0
    end
    multiples[iksnr][pacnr] = row
    row[@latest_keys.size] = idx
    known_regs.store [iksnr], row
    known_seqs.store [iksnr, seqnr], row
    known_pacs.store [iksnr, pacnr, idx], row
    (newest_rows[iksnr] ||= {})[pacnr] = row
  }
end

#_sort_by(sort, iksnr, flags) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 339

def _sort_by(sort, iksnr, flags)
  case sort
  when :name
    [name(@diff, iksnr), iksnr]
  when :registration
    iksnr
  else
    weight = if(flags.include? :new)
               0
             elsif(flags.include? :delete)
               1
             else
               2
             end
    [weight, iksnr]
  end
end

#capitalize(string) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 134

def capitalize(string)
  string.split(/\s+/).collect { |word| word.capitalize }.join(' ')
end

#cell(row, pos) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 137

def cell(row, pos)
  if(cell = row[pos])
    cell.to_s
  end
end

#describe(diff, iksnr) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 142

def describe(diff, iksnr)
  sprintf("%s: %s", iksnr, name(diff, iksnr))
end

#describe_flag(diff, iksnr, flag) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 145

def describe_flag(diff, iksnr, flag)
  txt = FLAGS.fetch(flag, flag)
  case flag
  when :sequence
  when :replaced_package
    pairs = diff.newest_rows[iksnr].collect { |rep, row|
      if(old = diff.replacements[row])
        [old, rep].join(' -> ')
      end
    }.compact
    sprintf "%s (%s)", txt, pairs.join(',')
  when :registration_date, :expiry_date
    row = diff.newest_rows[iksnr].sort.first.last
    if row[COLUMNS_2014.keys.index(flag)].value.to_s.match(REGEXP_UNLIMITED)
      sprintf "%s (%s)", txt, 'unbegrenzt'
    else
      sprintf "%s (%s)", txt, row[COLUMNS_2014.keys.index(flag)].value.strftime('%d.%m.%Y')
    end
  else
    row = diff.newest_rows[iksnr].sort.first.last
    sprintf "%s (%s)", txt, cell(row, COLUMNS_2014.keys.index(flag))
  end
end

#diff(target, latest, ignore = []) ⇒ Object

Comparison two Excel files

target

new file path (String)

latest

old file path (String)

ignore

columns not to be compared (Symbol)

return

differences (OpenStruct class)



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# File 'lib/swissmedic-diff.rb', line 176

def diff(target, latest, ignore = [])
  replacements = {}
  known_regs, known_seqs, known_pacs, newest_rows = known_data(latest)
  @diff = OpenStruct.new
  @diff.news = news = []
  @diff.updates = updates = []
  @diff.changes = changes = {}
  @diff.newest_rows = newest_rows
  Spreadsheet.client_encoding = 'UTF-8'
  tbook = Spreadsheet.open(target)
  idx, prr, prp = nil
  multiples = {}
  @latest_keys = get_column_indices(Spreadsheet.open(latest)).keys
  @target_keys = get_column_indices(tbook).keys
  each_valid_row(tbook) { |row|
    iksnr = cell(row, @target_keys.index(:iksnr))
    seqnr = cell(row, @target_keys.index(:seqnr))
    pacnr = cell(row, @target_keys.index(:ikscd))
    (multiples[iksnr] ||= {})
    if prr == iksnr && prp == pacnr
      idx += 1
    elsif previous = multiples[iksnr][pacnr]
      prr = iksnr
      prp = pacnr
      idx = previous[@target_keys.size].to_i + 1
    else
      prr = iksnr
      prp = pacnr
      idx = 0
    end
    row[@target_keys.size] = idx
    (newest_rows[iksnr] ||= {})[pacnr] = row
    multiples[iksnr][pacnr] = row
    if(other = known_regs.delete([iksnr]))
      changes[iksnr] ||= []
    else
      changes[iksnr] ||= [:new]
    end
    known_seqs.delete([iksnr, seqnr])
    if(other = known_pacs.delete([iksnr, pacnr, idx]))
      flags = rows_diff(row, other, ignore)
      (changes[iksnr].concat flags).uniq!
      updates.push row unless flags.empty?
    else
      replacements.store [ iksnr, seqnr, cell(row, @target_keys.index(:size)),
                            cell(row, @target_keys.index(:unit)) ], row
      flags = changes[iksnr]
      flags.push(:sequence).uniq! unless(flags.include? :new)
      news.push row
    end
  }
  @diff.replacements = reps = {}
  known_pacs.each { |(iksnr, pacnr), row|
    key = [iksnr, '%02i' % cell(row, @target_keys.index(:seqnr)).to_i,
                  cell(row, @target_keys.index(:size)), cell(row, @target_keys.index(:unit))]
    if(rep = replacements[key])
      changes[iksnr].push :replaced_package
      reps.store rep, pacnr
    end
  }
  known_regs.each_key { |(iksnr,_)| changes[iksnr] = [:delete] }
  changes.delete_if { |iksnr, flags| flags.empty? }
  @diff.package_deletions = known_pacs.collect { |key, row|
    ## the keys in known_pacs don't include the sequence number (which
    #  would prevent us from properly recognizing multi-sequence-Packages),
    #  so we need complete the path to the package now
    key[1,0] = '%02i' % cell(row, @target_keys.index(:seqnr)).to_i
    key
  }
  @diff.sequence_deletions = known_seqs.keys
  @diff.registration_deletions = known_regs.keys
  @diff
end

#each_valid_row(spreadsheet) ⇒ Object

iterate over all valid rows of a swissmedic Packungen.xls

Iterates over all rows, ignoring Tierarzneimittel and lines with not enough data Patches the fields :iksnr, :seqnr, :ikscd to match the old swissmedic convention of a fixed sized string

example:

SwissmedicDiff.new.each_valid_row(Spreadsheet.open('path/to/file')) { |x| puts "iksnr #{x[0]}" }
spreadsheet

spreadsheet to operate on

return 


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# File 'lib/swissmedic-diff.rb', line 448

def each_valid_row(spreadsheet)
  skipRows = rows_to_skip(spreadsheet)
  column_keys = get_column_indices(spreadsheet).keys
  worksheet = spreadsheet.worksheet(0)
  row_nr = 0
  worksheet.each() {
    |row|
    row_nr += 1
    next if row_nr <= skipRows
    break unless row
    if row.size < column_keys.size/2
      $stdout.puts "Data missing in \n(line " + (row_nr).to_s + "): " + row.join(", ").to_s + "\n"
      next
    end
    next if (cell(row, column_keys.index(:production_science)) == 'Tierarzneimittel')
    row[column_keys.index(:iksnr)] = "%05i" % cell(row, column_keys.index(:iksnr)).to_i
    row[column_keys.index(:seqnr)] = "%02i" % cell(row, column_keys.index(:seqnr)).to_i
    row[column_keys.index(:ikscd)] = "%03i" % cell(row, column_keys.index(:ikscd)).to_i
    yield row
  }
end

#format_flags(flags) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 249

def format_flags(flags)
  flags.delete(:revision)
  flags.collect { |flag|
    "- %s\n" % FLAGS.fetch(flag, "Unbekannt (#{flag})")
  }.compact.join
end

#get_column_indices(spreadsheet) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 373

def get_column_indices(spreadsheet)
  error_2014 = nil
  filename = spreadsheet.root.respond_to?(:filepath) ? spreadsheet.root.filepath : 'unknown'
  headerRowId = rows_to_skip(spreadsheet)-1
  row = spreadsheet.worksheet(0)[headerRowId]

  COLUMNS_2014.each{
    |key, value|
    header_name = row[COLUMNS_2014.keys.index(key)].value
    unless value.match(header_name)
      puts "#{__LINE__}: #{key} ->  #{COLUMNS_2014.keys.index(key)} #{value}\nbut was  #{header_name}" if $VERBOSE
      error_2014 = "#{filename}_has_unexpected_column_#{COLUMNS_2014.keys.index(key)}_#{key}_#{value.to_s}_but_was_#{header_name}"
      break
    end
  }
  return COLUMNS_2014 unless error_2014
  error_2015 = nil
  COLUMNS_JULY_2015.each{
    |key, value|
    header_name = row[COLUMNS_JULY_2015.keys.index(key)].value
    unless value.match(header_name)
      puts "#{__LINE__}: #{key} ->  #{COLUMNS_JULY_2015.keys.index(key)} #{value}\nbut was  #{header_name}" if $VERBOSE
      error_2015 = "#{filename}_has_unexpected_column_#{COLUMNS_JULY_2015.keys.index(key)}_#{key}_#{value.to_s}_but_was_#{header_name}"
      break
    end
  }
  unless error_2015
    idx14 = COLUMNS_2014.keys.index(:name_base)
    idx15 = COLUMNS_2014.keys.index(:name_base)
    if (idx14 != idx15)
      raise ":name_base must be same index in COLUMNS_JULY_2015 and COLUMNS_2014. Is #{idx14} and #{idx15}"
    end
    return COLUMNS_JULY_2015
  end
  row = spreadsheet.worksheet(0)[5] # Headers are found at row 5 since February 5
  error_2019 = nil
  if spreadsheet.worksheet(0)[5].size != COLUMNS_FEBRUARY_2019.size
    raise "#{error_2015}\n#{error_2014}"
  else
    0.upto((COLUMNS_FEBRUARY_2019.size) -1).each{ |idx| puts "#{idx}: #{row[idx].value}" }  if $VERBOSE
    COLUMNS_FEBRUARY_2019.each{
      |key, value|
      header_name = row[COLUMNS_FEBRUARY_2019.keys.index(key)].value.to_s
      unless value.match(header_name)
        puts "#{__LINE__}: #{key} ->  #{COLUMNS_FEBRUARY_2019.keys.index(key)} #{value}\nbut was  #{header_name}" if $VERBOSE
        error_2019 = "Packungen.xlslx_has_unexpected_column_#{COLUMNS_FEBRUARY_2019.keys.index(key)}_#{key}_#{value.to_s}_but_was_#{header_name}"
        require 'pry'; binding.pry
      break
      end
    }
    unless error_2015
      idx14 = COLUMNS_2014.keys.index(:name_base)
      idx15 = COLUMNS_2014.keys.index(:name_base)
      if (idx14 != idx15)
        raise ":name_base must be same index in COLUMNS_JULY_2015 and COLUMNS_2014. Is #{idx14} and #{idx15}"
      end
      return COLUMNS_FEBRUARY_2019
    end
    raise "#{error_2019}" if error_2019
 end
 COLUMNS_FEBRUARY_2019
end

#known_data(latest) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 255

def known_data(latest)
  known_regs = {}
  known_seqs = {}
  known_pacs = {}
  newest_rows = {}
  _known_data latest, known_regs, known_seqs, known_pacs, newest_rows
  [known_regs, known_seqs, known_pacs, newest_rows]
end

#name(diff, iksnr) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 292

def name(diff, iksnr)
  rows = diff.newest_rows[iksnr]
  row = rows.sort.first.last
  cell(row, COLUMNS_2014.keys.index(:name_base))
end

#rows_diff(row, other, ignore = []) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 297

def rows_diff(row, other, ignore = [])
  flags = []
  COLUMNS_OLD.each_with_index {
    |key, idx|
    if !ignore.include?(key)
      left  = _comparable(key, row,   @target_keys.index(key))
      right = _comparable(key, other, @latest_keys.index(key))
      next if left.is_a?(Date) && right.is_a?(Date) && left.strftime(DATE_FORMAT).eql?(right.strftime(DATE_FORMAT))
      next if left.is_a?(String) && left.empty? && !right
      next if right.is_a?(String) && right.empty? && !left
      if left != right
        flags.push key
      end
    end
  }
  flags
end

#rows_to_skip(spreadsheet) ⇒ Object 



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# File 'lib/swissmedic-diff.rb', line 470

def rows_to_skip(spreadsheet)
  # Packungen.xls of swissmedic before October 2013 had  3 leading rows
  # Packungen.xls of swissmedic after  October 2013 have 4 leading rows
  j = 0
  while true
    cell = spreadsheet.worksheet(0).row(j)[0]
    cell = cell.value if cell.is_a?(RubyXL::Cell)
    break if cell.respond_to?(:to_i) and cell.to_i != 0
    j += 1
  end
  j
end

#to_s(sort = :group) ⇒ Object

Output the differencies with String

This should be called after diff method.

sort

sort key (:group | :name | :registration)

return

difference (String)



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# File 'lib/swissmedic-diff.rb', line 322

def to_s(sort=:group)
  @diff ||= nil
  return '' unless @diff
  @diff.changes.sort_by { |iksnr, flags|
    _sort_by(sort, iksnr, flags)
  }.collect { |iksnr, flags|
    if(flags.include? :new)
      "+ " << describe(@diff, iksnr)
    elsif(flags.include? :delete)
      "- " << describe(@diff, iksnr)
    else
      "> " << describe(@diff, iksnr) << "; " \
        << flags.collect { |flag| describe_flag(@diff, iksnr, flag)
      }.compact.join(", ")
    end
  }.join("\n")
end