Gnumed.business.gmHL7 API documentation
Description: Some HL7 handling.

# Module `Gnumed.business.gmHL7`

Some HL7 handling.

## Functions

`def extract_HL7_from_XML_CDATA(filename, xml_path, target_dir=None)`
  Expand source code

      def extract_HL7_from_XML_CDATA(filename, xml_path, target_dir=None):

              _log.debug('extracting HL7 from CDATA of <%s> nodes in XML file [%s]', xml_path, filename)

              # sanity checks/setup
              try:
                      open(filename).close()
                      orig_dir = os.path.split(filename)[0]
                      work_filename = gmTools.get_unique_filename(prefix = 'gm-x2h-%s-' % gmTools.fname_stem(filename), suffix = '.hl7')
                      if target_dir is None:
                              target_dir = os.path.join(orig_dir, 'HL7')
                              done_dir = os.path.join(orig_dir, 'done')
                      else:
                              done_dir = os.path.join(target_dir, 'done')
                      _log.debug('target dir: %s', target_dir)
                      gmTools.mkdir(target_dir)
                      gmTools.mkdir(done_dir)
              except Exception:
                      _log.exception('cannot setup unwrapping environment')
                      return None

              hl7_xml = pyxml.ElementTree()
              try:
                      hl7_xml.parse(filename)
              except pyxml.ParseError:
                      _log.exception('cannot parse [%s]' % filename)
                      return None
              nodes = hl7_xml.findall(xml_path)
              if len(nodes) == 0:
                      _log.debug('no nodes found for data extraction')
                      return None

              _log.debug('unwrapping HL7 from XML into [%s]', work_filename)
              hl7_file = open(work_filename, mode = 'wt', encoding = 'utf8', newline = '')            # universal newlines acceptance but no translation on output
              for node in nodes:
      #               hl7_file.write(node.text.rstrip() + HL7_EOL)
                      hl7_file.write(node.text + '')          # trick to make node.text unicode
              hl7_file.close()

              target_fname = os.path.join(target_dir, os.path.split(work_filename)[1])
              shutil.copy(work_filename, target_dir)
              shutil.move(filename, done_dir)

              return target_fname

`def format_hl7_file(filename, skip_empty_fields=True, eol='\n ', return_filename=False, fix_hl7=True)`
  Expand source code

      def format_hl7_file(filename, skip_empty_fields=True, eol='\n ', return_filename=False, fix_hl7=True):
              if fix_hl7:
                      fixed_name = __fix_malformed_hl7_file(filename)
                      hl7_file = open(fixed_name, mode = 'rt', encoding = 'utf-8-sig', newline = '')  # read universal but pass on untranslated
                      source = '%s (<- %s)' % (fixed_name, filename)
              else:
                      hl7_file = open(filename, mode = 'rt', encoding = 'utf-8-sig', newline = '')    # read universal but pass on untranslated
                      source = filename
              output = format_hl7_message (
                      message = hl7_file.read(1024 * 1024 * 5),               # 5 MB max
                      skip_empty_fields = skip_empty_fields,
                      eol = eol,
                      source = source
              )
              hl7_file.close()

              if not return_filename:
                      return output

              max_len = 120
              if eol is None:
                      output = '\n '.join([ '%s: %s' % ((o[0] + (' ' * max_len))[:max_len], o[1]) for o in output ])

              out_name = gmTools.get_unique_filename(prefix = 'gm-formatted_hl7-', suffix = '.hl7')
              out_file = open(out_name, mode = 'wt', encoding = 'utf8')
              out_file.write(output)
              out_file.close()

              return out_name

`def format_hl7_message(message=None, skip_empty_fields=True, eol='\n ', source=None)`
  Expand source code

      def format_hl7_message(message=None, skip_empty_fields=True, eol='\n ', source=None):
              # a segment is a line starting with a type
              msg = pyhl7.parse(message)

              output = []
              if source is not None:
                      output.append([_('HL7 Source'), '%s' % source])
              output.append([_('HL7 data size'), _('%s bytes') % len(message)])
              output.append([_('HL7 Message'), _(' %s segments (lines)%s') % (len(msg), gmTools.bool2subst(skip_empty_fields, _(', skipping empty fields'), ''))])

              max_len = 0
              for seg_idx in range(len(msg)):
                      seg = msg[seg_idx]
                      seg_type = seg[0][0]

                      output.append([_('Segment #%s <%s>') % (seg_idx, seg_type), _('%s fields') % len(seg)])

                      for field_idx in range(len(seg)):
                              field = seg[field_idx]
                              try:
                                      label = HL7_field_labels[seg_type][field_idx]
                              except KeyError:
                                      label = _('HL7 %s field') % seg_type

                              max_len = max(max_len, len(label))

                              if len(field) == 0:
                                      if not skip_empty_fields:
                                              output.append(['%2s - %s' % (field_idx, label), _('<EMTPY>')])
                                      continue
                              if (len(field) == 1) and (('%s' % field[0]).strip() == ''):
                                      if not skip_empty_fields:
                                              output.append(['%2s - %s' % (field_idx, label), _('<EMTPY>')])
                                      continue

                              content_lines = ('%s' % field).split(HL7_BRK)
                              output.append(['%2s - %s' % (field_idx, label), content_lines[0]])
                              for line in content_lines[1:]:
                                      output.append(['', line])
                              #output.append([u'%2s - %s' % (field_idx, label), u'%s' % field])

              if eol is None:
                      return output

              max_len += 7
              return eol.join([ '%s: %s' % ((o[0] + (' ' * max_len))[:max_len], o[1]) for o in output ])

`def import_single_PID_hl7_file(filename)`
  Expand source code

      def import_single_PID_hl7_file(filename):

              log_name = '%s.import.log' % filename
              import_logger = logging.FileHandler(log_name)
              import_logger.setLevel(logging.DEBUG)
              root_logger = logging.getLogger('')
              root_logger.addHandler(import_logger)
              _log.debug('log file: %s', log_name)

              success = True
              try:
                      success = __import_single_PID_hl7_file(filename)
                      if not success:
                              _log.error('error when importing single-PID/single-MSH file')
              except Exception:
                      _log.exception('error when importing single-PID/single-MSH file')

              root_logger.removeHandler(import_logger)
              return success, log_name

`def process_staged_single_PID_hl7_file(staged_item)`
  Expand source code

      def process_staged_single_PID_hl7_file(staged_item):

              log_name = gmTools.get_unique_filename (
                      prefix = 'gm-staged_hl7_import-',
                      suffix = '.log'
              )
              import_logger = logging.FileHandler(log_name)
              import_logger.setLevel(logging.DEBUG)
              root_logger = logging.getLogger('')
              root_logger.addHandler(import_logger)
              _log.debug('log file: %s', log_name)

              if not staged_item.lock():
                      _log.error('cannot lock staged data for HL7 import')
                      root_logger.removeHandler(import_logger)
                      return False, log_name

              _log.debug('reference ID of staged HL7 data: %s', staged_item['external_data_id'])

              filename = staged_item.save_to_file()
              _log.debug('unstaged HL7 data into: %s', filename)

              if staged_item['pk_identity'] is None:
                      emr = None
              else:
                      emr = gmPerson.cPatient(staged_item['pk_identity']).emr

              success = False
              try:
                      success = __import_single_PID_hl7_file(filename, emr = emr)
                      if success:
                              gmIncomingData.delete_incoming_data(pk_incoming_data = staged_item['pk_incoming_data'])
                              staged_item.unlock()
                              root_logger.removeHandler(import_logger)
                              return True, log_name
                      _log.error('error when importing single-PID/single-MSH file')
              except Exception:
                      _log.exception('error when importing single-PID/single-MSH file')

              if not success:
                      staged_item['comment'] = _('failed import: %s\n') % gmDateTime.pydt_now_here().isoformat()
                      staged_item['comment'] += '\n'
                      staged_item['comment'] += ('-' * 80)
                      staged_item['comment'] += '\n\n'
                      log = open(log_name, mode = 'rt', encoding = 'utf-8-sig')
                      staged_item['comment'] += log.read()
                      log.close()
                      staged_item['comment'] += '\n'
                      staged_item['comment'] += ('-' * 80)
                      staged_item['comment'] += '\n\n'
                      staged_item['comment'] += format_hl7_file (
                              filename,
                              skip_empty_fields = True,
                              eol = '\n ',
                              return_filename = False
                      )
                      staged_item.save()

              staged_item.unlock()
              root_logger.removeHandler(import_logger)
              return success, log_name

`def split_hl7_file(filename, target_dir=None, encoding='utf8')`
  Expand source code

      def split_hl7_file(filename, target_dir=None, encoding='utf8'):
              """Multi-step processing of HL7 files.

              - input can be multi-MSH / multi-PID / partially malformed HL7
              - tries to fix oddities
              - splits by MSH
              - splits by PID into <target_dir>

              - needs write permissions in dir_of(filename)
              - moves HL7 files which were successfully split up into dir_of(filename)/done/

              - returns (True|False, list_of_PID_files)
              """
              local_log_name = gmTools.get_unique_filename (
                      prefix = gmTools.fname_stem(filename) + '-',
                      suffix = '.split.log'
              )
              local_logger = logging.FileHandler(local_log_name)
              local_logger.setLevel(logging.DEBUG)
              root_logger = logging.getLogger('')
              root_logger.addHandler(local_logger)
              _log.info('splitting HL7 file: %s', filename)
              _log.debug('log file: %s', local_log_name)

              # sanity checks/setup
              try:
                      open(filename).close()
                      orig_dir = os.path.split(filename)[0]
                      done_dir = os.path.join(orig_dir, 'done')
                      gmTools.mkdir(done_dir)
                      error_dir = os.path.join(orig_dir, 'failed')
                      gmTools.mkdir(error_dir)
                      work_filename = gmTools.get_unique_filename(prefix = gmTools.fname_stem(filename) + '-', suffix = '.hl7')
                      if target_dir is None:
                              target_dir = os.path.join(orig_dir, 'PID')
                      _log.debug('target dir: %s', target_dir)
                      gmTools.mkdir(target_dir)
              except Exception:
                      _log.exception('cannot setup splitting environment')
                      root_logger.removeHandler(local_logger)
                      return False, None

              # split
              target_names = []
              try:
                      shutil.copy(filename, work_filename)
                      fixed_filename = __fix_malformed_hl7_file(work_filename, encoding = encoding)
                      MSH_fnames = __split_hl7_file_by_MSH(fixed_filename, encoding)
                      PID_fnames = []
                      for MSH_fname in MSH_fnames:
                              PID_fnames.extend(__split_MSH_by_PID(MSH_fname))
                      for PID_fname in PID_fnames:
                              shutil.move(PID_fname, target_dir)
                              target_names.append(os.path.join(target_dir, os.path.split(PID_fname)[1]))
              except Exception:
                      _log.exception('cannot split HL7 file')
                      for target_name in target_names:
                              try: os.remove(target_name)
                              except Exception: pass
                      root_logger.removeHandler(local_logger)
                      shutil.move(local_log_name, error_dir)
                      return False, None

              _log.info('successfully split')
              root_logger.removeHandler(local_logger)
              try:
                      shutil.move(filename, done_dir)
                      shutil.move(local_log_name, done_dir)
              except shutil.Error:
                      _log.exception('cannot move hl7 file or log file to holding area')
              return True, target_names

  Multi-step processing of HL7 files.

  - input can be multi-MSH / multi-PID / partially malformed HL7
  - tries to fix oddities
  - splits by MSH

  - splits by PID into

  - needs write permissions in dir_of(filename)

  - moves HL7 files which were successfully split up into dir_of(filename)/done/

  - returns (True|False, list_of_PID_files)

`def stage_single_PID_hl7_file(filename, source=None, encoding='utf8')`
  Expand source code

      def stage_single_PID_hl7_file(filename, source=None, encoding='utf8'):
              """Multi-step processing of HL7 files.

              - input must be single-MSH / single-PID / normalized HL7

              - imports into clin.incoming_data

              - needs write permissions in dir_of(filename)
              - moves PID files which were successfully staged into dir_of(filename)/done/PID/
              """
              local_log_name = gmTools.get_unique_filename (
                      prefix = gmTools.fname_stem(filename) + '-',
                      suffix = '.stage.log'
              )
              local_logger = logging.FileHandler(local_log_name)
              local_logger.setLevel(logging.DEBUG)
              root_logger = logging.getLogger('')
              root_logger.addHandler(local_logger)
              _log.info('staging [%s] as unmatched incoming HL7%s', filename, gmTools.coalesce(source, '', ' (%s)'))
              _log.debug('log file: %s', local_log_name)

              # sanity checks/setup
              try:
                      open(filename).close()
                      orig_dir = os.path.split(filename)[0]
                      done_dir = os.path.join(orig_dir, 'done')
                      gmTools.mkdir(done_dir)
                      error_dir = os.path.join(orig_dir, 'failed')
                      gmTools.mkdir(error_dir)
              except Exception:
                      _log.exception('cannot setup staging environment')
                      root_logger.removeHandler(local_logger)
                      return False

              # stage
              try:
                      incoming = gmIncomingData.create_incoming_data('HL7%s' % gmTools.coalesce(source, '', ' (%s)'), filename)
                      if incoming is None:
                              _log.error('cannot stage PID file: %s', filename)
                              root_logger.removeHandler(local_logger)
                              shutil.move(filename, error_dir)
                              shutil.move(local_log_name, error_dir)
                              return False
                      incoming.update_data_from_file(fname = filename)
              except Exception:
                      _log.exception('error staging PID file')
                      root_logger.removeHandler(local_logger)
                      shutil.move(filename, error_dir)
                      shutil.move(local_log_name, error_dir)
                      return False

              # set additional data
              MSH_file = open(filename, mode = 'rt', encoding = 'utf-8-sig', newline = '')
              raw_hl7 = MSH_file.read(1024 * 1024 * 5)        # 5 MB max
              MSH_file.close()
              shutil.move(filename, done_dir)
              incoming['comment'] = format_hl7_message (
                      message = raw_hl7,
                      skip_empty_fields = True,
                      eol = '\n'
              )
              HL7 = pyhl7.parse(raw_hl7)
              del raw_hl7
              incoming['comment'] += '\n'
              incoming['comment'] += ('-' * 80)
              incoming['comment'] += '\n\n'
              log = open(local_log_name, mode = 'rt', encoding = 'utf-8-sig')
              incoming['comment'] += log.read()
              log.close()
              try:
                      incoming['lastnames'] = HL7.extract_field('PID', segment_num = 1, field_num = PID_field__name, component_num = PID_component__lastname)
                      incoming['firstnames'] = HL7.extract_field('PID', segment_num = 1, field_num = PID_field__name, component_num = PID_component__firstname)
                      val = HL7.extract_field('PID', segment_num = 1, field_num = PID_field__name, component_num = PID_component__middlename)
                      if val is not None:
                              incoming['firstnames'] += ' '
                              incoming['firstnames'] += val
                      val = HL7.extract_field('PID', segment_num = 1, field_num = PID_field__dob)
                      if val is not None:
                              tmp = time.strptime(val, '%Y%m%d')
                              incoming['dob'] = pyDT.datetime(tmp.tm_year, tmp.tm_mon, tmp.tm_mday, tzinfo = gmDateTime.gmCurrentLocalTimezone)
                      val = HL7.extract_field('PID', segment_num = 1, field_num = PID_field__gender)
                      if val is not None:
                              incoming['gender'] = val
                      incoming['external_data_id'] = filename
                      #u'fk_patient_candidates',
                      #       u'request_id',                                          # request ID as found in <data>
                      #       u'postcode',
                      #       u'other_info',                                          # other identifying info in .data
                      #       u'requestor',                                           # Requestor of data (e.g. who ordered test results) if available in source data.
                      #       u'fk_identity',
                      #       u'comment',                                                     # a free text comment on this row, eg. why is it here, error logs etc
                      #       u'fk_provider_disambiguated'            # The provider the data is relevant to.
              except Exception:
                      _log.exception('cannot add more data')
              incoming.save()

              _log.info('successfully staged')
              root_logger.removeHandler(local_logger)
              shutil.move(local_log_name, done_dir)
              return True

  Multi-step processing of HL7 files.

  - input must be single-MSH / single-PID / normalized HL7

  - imports into clin.incoming_data

  - needs write permissions in dir_of(filename)

  - moves PID files which were successfully staged into dir_of(filename)/done/PID/