Class: ProfileParser

Inherits:
Object
  • Object
show all
Includes:
Utils
Defined in:
lib/ez7gen/profile_parser.rb

Constant Summary collapse

FILTER_ADM = 
{filter: 'ADT_A|QBP_Q2|RSP_K2[1-4]', group: 'Admissions'}
FILTER_FM = 
{filter: 'DFT_P03|DFT_P11|DFT_X03', group: 'Financial Management'}
FILTER_GEN = 
{filter: 'OSR_Q06|OSQ_Q06|ORG_O20|OMG_O19', group: 'General'}
FILTER_LAB = 
{filter: 'ORL_O22|OML_O21|QRY_R02|OUL_R21|ORU_R01', group: 'Laboratory'}
FILTER_MSR = 
{filter: 'MFN_M01|MFN_X01|MFN_Y01', group: 'Master Files'}
FILTER_OBS = 
{filter: 'OMS_O05', group: 'Order'}
FILTER_PH = 
{filter: 'OMP_|ORP_|RDE_|RRE_|RDS_|RRD_|RGV_|RRG_|RAS_|RRA_', group: 'Pharmacy'}
@@FILTER_ALL =

attr_reader :xml;

{filter: '.*', group: 'All'}
@@segment_patern =

attr_accessor :std; :version; :event; :xml; :version_store; @@HL7_VERSIONS = ‘vaz2.4’=>‘vaz2.4/vaz2.4-schema.xml’ class attribute @@segment_patern = /[([^[]]*)]/

/\[([^\[\]]*)\]|\{([^\[\]]*)\}/

Constants included from Utils

Utils::BASE, Utils::BASE_INDICATOR, Utils::DATA_LOOKUP_MIS, Utils::PRIMARY

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Utils

#blank?, #get_name_without_base, #get_segment_name, #get_type_by_name, #has_html_encoded_ch?, #is_number?, #num_to_nil, #safe_len, #sample_index

Constructor Details

#initialize(args) ⇒ ProfileParser

Child class has a wrapper TODO: Refactor def initialize(version=nil, event=nil)



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# File 'lib/ez7gen/profile_parser.rb', line 31

def initialize(args)
  args.each do |k,v|
    instance_variable_set("@#{k}", v) unless v.nil?
  end
  # set to false if it has not been set already
  # @base ||= false

  profile, path = nil
  # if(@version_store)
    profile = @version_store.find{|v| v[:std] == @std}[:profiles].find{|p| p[:doc] == @version }[:path]
    path = @version_store.detect{|v| v[:std] == @std}[:path]
  # else
  #   # path = self.class.get_schema_location
  #   # profile = File.path(path+ @@HL7_VERSIONS[@version])
  # end

  @xml = Ox.parse(IO.read(profile))

  # added = File.path(path+'added.xml')
  begin
    added = File.path(path+'/added/coded-tables.xml')
    @added = Ox.parse(IO.read(added))
  rescue => e
    # puts e.message
    $log.error ("#{self.class.to_s}:#{__method__.to_s}") { e.message }


  end

  # set flag if this is base or custom schema
  @base = (@xml.Export.Document.Category.attributes[:std] == '1')

end

Instance Attribute Details

#base ⇒ Object (readonly) Also known as: base?

instance attributes



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# File 'lib/ez7gen/profile_parser.rb', line 9

def base
  @base
end

#xml ⇒ Object (readonly)

instance attributes



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# File 'lib/ez7gen/profile_parser.rb', line 9

def xml
  @xml
end

Class Method Details

.get_schema_location ⇒ Object

instance methods



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# File 'lib/ez7gen/profile_parser.rb', line 66

def self.get_schema_location
  #properties_file = File.expand_path('../resources/properties.yml', __FILE__)
  #yml = YAML.load_file properties_file
  #path = yml['web.install.dir'] # set when run intall gem with argument, example: gem install 'c:/ez7Gen/ez7gen-web/config/resources/'
  path = File.expand_path('../', __FILE__)
  path = File.join(path, 'config/schema/')
  #puts path + ' : self.get_schema_location'
    # path = path<<'config/schema/'
  # path = path<<'config/resources/'
end

.getExclusionFilterRule(std, version) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 100

def self.getExclusionFilterRule(std, version)
  path = self.get_schema_location
  rules_file = "#{path}#{std}/rules/#{version}.yml"

  if File.exists? (rules_file)
    yml = YAML.load_file rules_file
    all = []
    all += (yml['exclusion.errors'])?yml['exclusion.errors']:[]
    all += (yml['exclusion.blacklist'])?yml['exclusion.blacklist']:[]
  else
    []
  end

end

.getVersionUrlRule(std, version) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 114

def self.getVersionUrlRule(std, version)
  path = self.get_schema_location
  rules_file = "#{path}#{std}/rules/#{version}.yml"

  if File.exists? (rules_file)
    yml = YAML.load_file rules_file
    (yml['version.url'])?yml['version.url']:nil
  else
    nil
  end

end

.lookup_versions ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 77

def self.lookup_versions
  path = self.get_schema_location
  puts path + " self.lookup_versions"
  names = Dir.glob("#{path}*").select {|f| File.directory? f}
  versions = names.map{|it| { std: it.sub(path,''), path: it}}
  # for each version
  # look get list of .xml files, except added,own directory for added?
  versions.each{|version|
    profiles = []

    Dir.glob("#{version[:path]}/**").select {|file| !File.directory? file}.each{|path|
      xml = Ox.parse(IO.read(path))
      # for each schema collect metadata
      profile = xml.Export.Document.attributes
      profile[:doc] = profile.delete(:name) # resolve collision with same keys
      profile.merge!(xml.Export.Document.Category.attributes)
      profile[:path] = path
      profiles << profile
    }
    version[:profiles] = profiles
  }
end

Instance Method Details

#build_event_attributes(event, templates, path) ⇒ Object

build all the details for event type including template information



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# File 'lib/ez7gen/profile_parser.rb', line 247

def build_event_attributes(event, templates, path)

  attr = {}
  attr[:name] = event
  #chek if there is a match otherwise use the segment name
  attr[:code] = get_message_event_desc(event)

  # check if this event has matching template files
  # event_templates = templates.collect { |template| template =~/#{event}/ } unless blank?(templates)
  # attr[:templates] = templates unless blank?(event_templates)
  if (!blank?(templates))
    # try to match templates to an event by name
    event_templates = templates.select { |template| template =~/#{event}/i }
    # if found set event attribute with template names
    if(!blank?(event_templates))

       # attr[:templates] = []
       #update event code with template count
      #code = "<b> +#{event_templates.size}" << (event_templates.size == 1) ? "TEMPLATE" : "TEMPLATES" << "</b>"
      # attr[:code] += "<div><b><font color=#337ab7>#{event_templates.size} #{(event_templates.size == 1) ? 'TEMPLATE' : 'TEMPLATES'}</font></b></div>"
      attr[:code] += "<small><b><font color=#337ab7> (#{event_templates.size}#{(event_templates.size == 1) ? 'TEMPLATE' : 'TEMPLATES'})</font></b></small>"
      # if (event_templates.size == 1) then code.chop! end
      # attr[:code] += "#{code}"

      # if (event_templates.size == 1) then attr[:code].chop! end

       attr[:templates] = event_templates.collect{ |tmpl|
         desc = Ox.parse(IO.read("#{path}/#{tmpl}")).HL7v2xConformanceProfile.HL7v2xStaticDef.attributes[:EventDesc]
         # desc = (!blank?(desc)) ? desc : "Custom #{event}"
         desc = (!blank?(desc)) ? desc : tmpl.gsub('_',' ').sub('.xml','')
         {:desc => desc.upcase , :file => tmpl}
       }
    end

  end


 return attr
end

#get_code_table(tableName) ⇒ Object

get hash of attributes for codeTable values



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# File 'lib/ez7gen/profile_parser.rb', line 165

def get_code_table(tableName)
  #exclude 361,362 sending/receiving app and facility
  #if(tableName in ['72','88','132','264','269','471','9999']){
  #	println tableName
  #}

  #empty hash if no table name
  return [] if blank?(tableName)

  attributes = lookup_code_table(tableName, @xml)

  if(blank?(attributes))||(attributes.size == 1  && attributes[0][:value] =='...')
    attributes = lookup_code_table(tableName, @added)
  end

  # Per Galina, code table values with special characters. Ensemble validation fails.
  # Filter out codes which have html encoded characters - Ensemble has problem handling it.
  # a bit of awkward logic - if either description or value has html encoded chars, remove the item
  attributes.select!{|a| (has_html_encoded_ch?(a[:description]) || has_html_encoded_ch?(a[:value]))?false:true }

  return attributes
end

#get_message_definition ⇒ Object

find message structure by event type



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# File 'lib/ez7gen/profile_parser.rb', line 128

def get_message_definition
  msg_type = get_message_structure(@event)
  # p msg_type
  $log.info("#{self.class.to_s}:#{__method__.to_s}") { msg_type }
  definition = @xml.Export.Document.Category.locate('MessageStructure').select{|it| it.attributes[:name] == msg_type }.first.attributes[:definition]
  post_process(definition)
end

#get_message_event_desc(event) ⇒ Object

look up for event description



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# File 'lib/ez7gen/profile_parser.rb', line 298

def get_message_event_desc(event)
  desc = nil
  tbl = @xml.Export.Document.Category.locate('CodeTable').select { |it| (it.attributes[:description] == 'Event type') }

  if(!blank?(tbl))
    # get event/message name ex: NO2 for ACK_NO2
    event_name = (event.split('_')).last
    for t in tbl # could be multiple tables, iterate
      desc = (( e = t.locate('Enumerate').select{ |it| it.attributes[:value] == event_name }); e!=[])? (e.first().attributes[:description]) : nil
      if(desc)then break end # brake after first match
    end # for
  end # if

  return desc || event
end

#get_message_structure(event) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 159

def get_message_structure(event)
  msg_type = @xml.Export.Document.Category.locate('MessageType').select { |it| it.attributes[:name] == event }.first.attributes[:structure]
end

#get_segment_structure(segment) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 193

def get_segment_structure(segment)
  segmentName = get_segment_name(segment)
  # $log.info (segment)
  $log.info("#{self.class.to_s}:#{__method__.to_s}") { segment }
  # node = export.Document.Category.SegmentStructure.find{ it.@name == segmentName}
  # values = @xml.elements.collect("Export/Document/Category/SegmentStructure[@name ='#{segmentName}']/SegmentSubStructure"){|x| x.attributes}
  @xml.Export.Document.Category.locate('SegmentStructure').select{|it| it.attributes[:name] == segmentName }.first.locate('SegmentSubStructure').map{|it| it.attributes}
  #values.each {|it| puts it}
end

#get_templates(path) ⇒ Object

# look up for message template files in a specified directory



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# File 'lib/ez7gen/profile_parser.rb', line 288

def get_templates(path)
  begin
    Dir.entries(path).select {|f| f =~/.xml/i}.sort
  # rescue => e
  rescue
    [] # handle case when dir is missing
  end
end

#lookup_code_table(tableName, path) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 188

def lookup_code_table(tableName, path)
  tbl = path.Export.Document.Category.locate('CodeTable').select { |it| it.attributes[:name] == tableName }
  (!blank?(tbl)) ? tbl.first.locate('Enumerate').map { |it| it.attributes } : [Utils::DATA_LOOKUP_MIS]
end

#lookup_events(params) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 224

def lookup_events(params)

  #all events for version
  events = @xml.Export.Document.Category.locate('MessageType').map!{|it| it.attributes[:name]}

  #if there are exclusion rule, remove the exclusions
  if(!blank?(params[:exclusions]))
    events -= params[:exclusions]
  end

  path = params[:templates_path]

  templates = (!blank?(path))? get_templates(path) : []

  # go over the events and build attributes of the array
  events_with_attr = events.map{ |el|
    build_event_attributes(el, templates, path)
  }

  #events_with_attr
end

#lookup_message_groups(groups) ⇒ Object

helper method to look up messages for specific groups of messages



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# File 'lib/ez7gen/profile_parser.rb', line 315

def lookup_message_groups (groups)
  messages = []
  groups.each{ |group| messages += lookup_message_types(group) }
  return messages
end

#lookup_message_types(map = nil, exclusion = nil) ⇒ Object 



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# File 'lib/ez7gen/profile_parser.rb', line 203

def lookup_message_types(map=nil, exclusion=nil)
  # match everything if no filter defined
  map ||= @@FILTER_ALL

  filter = map[:filter]
  messageTypeColl = @xml.Export.Document.Category.locate('MessageType').select{|it| it.attributes[:name] =~/#{filter}/}.map!{|it| it.attributes[:name]}
  if(!blank?(exclusion))
    messageTypeColl = messageTypeColl - exclusion
  end
  messages = messageTypeColl.map{ |el|
    event = (el.split('_')).last
     {
        name: el,
        #chek if there is a match otherwise use the segment name
        code: ((e = @xml.Export.Document.Category.locate('MessageEvent').select{|it| it.attributes[:name] == event}); e!=[] )? (e.first().attributes[:description]): el,
        group: map[:group]
    }
  }
  return messages
end

#post_process(definition) ⇒ Object

helper method to handle corner cases



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# File 'lib/ez7gen/profile_parser.rb', line 137

def post_process(definition)

  if(@base && (@event == 'OSR_Q06'))
    # 1.If the OSQ_O06 query is about the status of the general messages OMG_O19 General Clinical Order and OML_O21 Lab Order, which only have the OBR segment, then the OSR_O06 should only have the OBR segment in its Order Detail Segment <   >.
    # 2.If the OSQ_O06 query is about the status of the Pharmacy order messages (OMP_O09, RDE_O11) that do not have OBR segment, but have RXO segment, then the OSR_O06 Order Detail Segment <     > should only contain RXO.
    # definition.sub!(/<(.*?)>/,['OBR','RXO'].sample())
    # puts definition
    definition = definition.sub!(/<(.*?)>/,['OBR','RXO'].sample())
    # puts definition
  elsif(@base && (@event == 'ORL_O22'))
    # work around for Ensemble issue where repeating group causes error in validation, remove repeating {} tag
    # MSH~MSA~[~ERR~]~[~{~NTE~}~]~[~[~PID~{~[~SAC~[~{~OBX~}~]~]~[~{~ORC~[~OBR~[~{~SAC~}~]~]~}~]~}~]~]
    # 'MSH~MSA~[~ERR~]~[~{~NTE~}~]~[~PID~{~[~SAC~[~{~OBX~}~]~]~[~{~ORC~[~OBR~[~{~SAC~}~]~]~}~]~}~]' #simplified
    # 'MSH~MSA~[~ERR~]~[~{~NTE~}~]~[~PID~[~[~SAC~[~{~OBX~}~]~]~[~{~ORC~[~OBR~[~{~SAC~}~]~]~}~]~]~]' #changed
    definition = 'MSH~MSA~[~ERR~]~[~{~NTE~}~]~[~PID~[~[~SAC~[~{~OBX~}~]~]~[~{~ORC~[~OBR~[~{~SAC~}~]~]~}~]~]~]'
    # definition.sub('[~{~ORC~[~OBR~[~{~SAC~}~]~]~}~]', '[~ORC~[~OBR~[~{~SAC~}~]~]~]')
  else
    definition
  end
    return definition
end