Gnumed.business.gmSOAPimporter API documentation
Description: GNUmed SOAP importer …

# Module `Gnumed.business.gmSOAPimporter`

GNUmed SOAP importer

(specification by Karsten Hilbert Karsten.Hilbert@gmx.net)

This script is designed for importing GNUmed SOAP input "bundles".

        - "bundle" is list of dicts
        - each "bundle" is processed dict by dict
        - the dicts in the list are INDEPENDENT of each other
        - each dict contains information for one new clin_narrative row
        - each dict has the keys: 'soap', 'types', 'text', 'clin_context'
                - 'soap':
                        - relates to clin_narrative.soap_cat
                - 'types':
                        - a list of strings
                        - the strings must be found in clin_item_type.type
                        - strings not found in clin_item_type.type are ignored during
                          import and the user is warned about that
                - 'text':
                        - the narrative for clin_narrative.narrative, imported as is
                - 'clin_context':
                        - 'clin_context' is a dictionary containing clinical
                          context information, required to properly create clinical items.
                          Its 'episode_id' must always be supplied.

Expand source code

    """GNUmed SOAP importer

    (specification by Karsten Hilbert <Karsten.Hilbert@gmx.net>)

    This script is designed for importing GNUmed SOAP input "bundles".

            - "bundle" is list of dicts
            - each "bundle" is processed dict by dict
            - the dicts in the list are INDEPENDENT of each other
            - each dict contains information for one new clin_narrative row
            - each dict has the keys: 'soap', 'types', 'text', 'clin_context'
                    - 'soap':
                            - relates to clin_narrative.soap_cat
                    - 'types':
                            - a list of strings
                            - the strings must be found in clin_item_type.type
                            - strings not found in clin_item_type.type are ignored during
                              import and the user is warned about that
                    - 'text':
                            - the narrative for clin_narrative.narrative, imported as is
                    - 'clin_context':
                            - 'clin_context' is a dictionary containing clinical
                              context information, required to properly create clinical items.
                              Its 'episode_id' must always be supplied.
    """
    #===============================================================
    __author__ = "Carlos Moro <cfmoro1976@yahoo.es>"
    __license__ = "GPL v2 or later (details at https://www.gnu.org)"

    # stdlib
    import sys, logging

    # GNUmed
    from Gnumed.pycommon import gmDispatcher
    from Gnumed.business import gmClinNarrative, gmPerson, gmPersonSearch

    _log = logging.getLogger('gm.soap')

    # module level constants
    soap_bundle_SOAP_CAT_KEY = "soap"
    soap_bundle_TYPES_KEY = "types"
    soap_bundle_TEXT_KEY = "text"
    soap_bundle_CLIN_CTX_KEY = "clin_context"
    soap_bundle_TYPE_KEY = "type"
    soap_bundle_EPISODE_ID_KEY = "episode_id"
    soap_bundle_ENCOUNTER_ID_KEY = "encounter_id"
    soap_bundle_STAFF_ID_KEY = "staff_id"
    soap_bundle_SOAP_CATS = ['s','o','a','p']               # these are pretty much fixed
    #===============================================================
    class cSOAPImporter:
            """
            Main SOAP importer class
            """
            #-----------------------------------------------------------
            def __init__(self):
                    pass
            #-----------------------------------------------------------
            # external API
            #-----------------------------------------------------------
            def import_soap(self, bundle=None):
                    """
                    Import supplied GNUmed SOAP input "bundle". For details consult current
                    module's description information.

                    @param bundle: GNUmed SOAP input data (as described in module's information)
                    @type bundle: list of dicts
                    """
                    # process each entry in soap bundle independently
                    for soap_entry in bundle:
                            if not self.__import_narrative(soap_entry):
                                    _log.error('skipping soap entry')
                                    continue
                    gmDispatcher.send(signal = 'clin_item_updated')
                    return True
            #-----------------------------------------------------------
            # internal helpers
            #-----------------------------------------------------------
            def __import_narrative(self, soap_entry):
                    """Import soap entry into GNUmed backend.

                    @param soap_entry: dictionary containing information related
                                                       to one SOAP input line
                    @type soap_entry: dictionary with keys 'soap', 'types', 'text'

                    FIXME: Later we may want to allow for explicitly setting a staff ID to be
                    FIXME: used for import. This would allow to import data "on behalf of" someone.
                    """
                    if not self.__verify_soap_entry(soap_entry=soap_entry):
                            _log.error('cannot verify soap entry')
                            return False
                    # obtain clinical context information
                    emr = gmPerson.gmCurrentPatient().emr
                    epi_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
                    try:
                            enc_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_ENCOUNTER_ID_KEY]
                    except KeyError:
                            enc = emr.active_encounter
                            enc_id = enc['pk_encounter']

                    # create narrative row
                    narr = gmClinNarrative.create_narrative_item (
                            narrative = soap_entry[soap_bundle_TEXT_KEY],
                            soap_cat = soap_entry[soap_bundle_SOAP_CAT_KEY],
                            episode_id = epi_id,
                            encounter_id = enc_id
                    )

    #               # attach types
    #               if soap_bundle_TYPES_KEY in soap_entry:
    #                       print "code missing to attach types to imported narrative"

                    return (narr is not None)
            #-----------------------------------------------------------
            def __verify_soap_entry(self, soap_entry):
                    """Perform basic integrity check of a supplied SOAP entry.

                    @param soap_entry: dictionary containing information related to one
                                                       SOAP input
                    @type soap_entry: dictionary with keys 'soap', 'types', 'text'
                    """
                    required_keys = [
                            soap_bundle_SOAP_CAT_KEY,
                            soap_bundle_CLIN_CTX_KEY,
                            soap_bundle_TEXT_KEY
                    ]
                    # verify key existence
                    for a_key in required_keys:
                            try:
                                    soap_entry[a_key]
                            except KeyError:
                                    _log.error('key [%s] is missing from soap entry' % a_key)
                                    _log.error('%s' % soap_entry)
                                    return False
                    # verify key *values*
                    if not soap_entry[soap_bundle_SOAP_CAT_KEY] in soap_bundle_SOAP_CATS:
                            _log.error('invalid soap category [%s]' % soap_entry[soap_bundle_SOAP_CAT_KEY])
                            _log.error('%s' % soap_entry)
                            return False
                    try:
                            soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
                    except KeyError:
                            _log.error('SOAP entry does not provide mandatory episode ID')
                            _log.error('%s' % soap_entry)
                            return False
                    return True
            #-----------------------------------------------------------
    #       def _verify_types(self, soap_entry):
    #               """
    #               Perform types key check of a supplied SOAP entry
    #
    #               @param soap_entry: dictionary containing information related to one
    #                                                  SOAP input
    #               @type soap_entry: dictionary with keys 'soap', 'types', 'text'
    #               """
    #
    #               # FIXME fetch from backend
    #               allowed_types = ['Hx']
    #               for input_type in soap_entry[soap_bundle_TYPES_KEY]:
    #                       if not input_type in allowed_types:
    #                               _log.error('bad clin_item_type.type in supplied soap entry [%s]' %
    #                               soap_entry)
    #                               return False
    #               return True

    #================================================================
    # MAIN
    #----------------------------------------------------------------
    if __name__ == '__main__':
            _log.info("starting SOAP importer...")

            # obtain patient
            patient = gmPersonSearch.ask_for_patient()
            if patient is None:
                    print("No patient. Exiting gracefully...")
                    sys.exit(0)
            gmPerson.set_active_patient(patient=patient)

            # now import
            importer = cSOAPImporter()
            bundle = [
                    {soap_bundle_SOAP_CAT_KEY: 's',
                     soap_bundle_TYPES_KEY: ['Hx'],
                     soap_bundle_TEXT_KEY: 'Test subjective narrative',
                     soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
                    },
                    {soap_bundle_SOAP_CAT_KEY: 'o',
                     soap_bundle_TYPES_KEY: ['Hx'],
                     soap_bundle_TEXT_KEY: 'Test objective narrative',
                     soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
                    },
                    {soap_bundle_SOAP_CAT_KEY: 'a',
                     soap_bundle_TYPES_KEY: ['Hx'],
                     soap_bundle_TEXT_KEY: 'Test assesment narrative',
                     soap_bundle_CLIN_CTX_KEY: {soap_bundle_EPISODE_ID_KEY: '1'}
                    },
                    {soap_bundle_SOAP_CAT_KEY: 'p',
                     soap_bundle_TYPES_KEY: ['Hx'],
                     soap_bundle_TEXT_KEY: 'Test plan narrative. [:tetanus:]. [:pneumoniae:].',
                     soap_bundle_CLIN_CTX_KEY: {
                            soap_bundle_EPISODE_ID_KEY: '1',
                            soap_bundle_ENCOUNTER_ID_KEY: '1',
                            soap_bundle_STAFF_ID_KEY: '1'
                            },
                    }
            ]
            importer.import_soap(bundle)

            # clean up
            if patient is not None:
                    try:
                            patient.cleanup()
                    except Exception:
                            print("error cleaning up patient")

            _log.info("closing SOAP importer...")
    #================================================================

## Classes

`class cSOAPImporter`

  Main SOAP importer class

  Expand source code

      class cSOAPImporter:
              """
              Main SOAP importer class
              """
              #-----------------------------------------------------------
              def __init__(self):
                      pass
              #-----------------------------------------------------------
              # external API
              #-----------------------------------------------------------
              def import_soap(self, bundle=None):
                      """
                      Import supplied GNUmed SOAP input "bundle". For details consult current
                      module's description information.

                      @param bundle: GNUmed SOAP input data (as described in module's information)
                      @type bundle: list of dicts
                      """
                      # process each entry in soap bundle independently
                      for soap_entry in bundle:
                              if not self.__import_narrative(soap_entry):
                                      _log.error('skipping soap entry')
                                      continue
                      gmDispatcher.send(signal = 'clin_item_updated')
                      return True
              #-----------------------------------------------------------
              # internal helpers
              #-----------------------------------------------------------
              def __import_narrative(self, soap_entry):
                      """Import soap entry into GNUmed backend.

                      @param soap_entry: dictionary containing information related
                                                         to one SOAP input line
                      @type soap_entry: dictionary with keys 'soap', 'types', 'text'

                      FIXME: Later we may want to allow for explicitly setting a staff ID to be
                      FIXME: used for import. This would allow to import data "on behalf of" someone.
                      """
                      if not self.__verify_soap_entry(soap_entry=soap_entry):
                              _log.error('cannot verify soap entry')
                              return False
                      # obtain clinical context information
                      emr = gmPerson.gmCurrentPatient().emr
                      epi_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
                      try:
                              enc_id = soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_ENCOUNTER_ID_KEY]
                      except KeyError:
                              enc = emr.active_encounter
                              enc_id = enc['pk_encounter']

                      # create narrative row
                      narr = gmClinNarrative.create_narrative_item (
                              narrative = soap_entry[soap_bundle_TEXT_KEY],
                              soap_cat = soap_entry[soap_bundle_SOAP_CAT_KEY],
                              episode_id = epi_id,
                              encounter_id = enc_id
                      )

      #               # attach types
      #               if soap_bundle_TYPES_KEY in soap_entry:
      #                       print "code missing to attach types to imported narrative"

                      return (narr is not None)
              #-----------------------------------------------------------
              def __verify_soap_entry(self, soap_entry):
                      """Perform basic integrity check of a supplied SOAP entry.

                      @param soap_entry: dictionary containing information related to one
                                                         SOAP input
                      @type soap_entry: dictionary with keys 'soap', 'types', 'text'
                      """
                      required_keys = [
                              soap_bundle_SOAP_CAT_KEY,
                              soap_bundle_CLIN_CTX_KEY,
                              soap_bundle_TEXT_KEY
                      ]
                      # verify key existence
                      for a_key in required_keys:
                              try:
                                      soap_entry[a_key]
                              except KeyError:
                                      _log.error('key [%s] is missing from soap entry' % a_key)
                                      _log.error('%s' % soap_entry)
                                      return False
                      # verify key *values*
                      if not soap_entry[soap_bundle_SOAP_CAT_KEY] in soap_bundle_SOAP_CATS:
                              _log.error('invalid soap category [%s]' % soap_entry[soap_bundle_SOAP_CAT_KEY])
                              _log.error('%s' % soap_entry)
                              return False
                      try:
                              soap_entry[soap_bundle_CLIN_CTX_KEY][soap_bundle_EPISODE_ID_KEY]
                      except KeyError:
                              _log.error('SOAP entry does not provide mandatory episode ID')
                              _log.error('%s' % soap_entry)
                              return False
                      return True
              #-----------------------------------------------------------

  ### Methods

  `def import_soap(self, bundle=None)`

    Import supplied GNUmed SOAP input "bundle". For details consult current module's description information.

    @param bundle: GNUmed SOAP input data (as described in module's information) @type bundle: list of dicts

    Expand source code

        def import_soap(self, bundle=None):
                """
                Import supplied GNUmed SOAP input "bundle". For details consult current
                module's description information.

                @param bundle: GNUmed SOAP input data (as described in module's information)
                @type bundle: list of dicts
                """
                # process each entry in soap bundle independently
                for soap_entry in bundle:
                        if not self.__import_narrative(soap_entry):
                                _log.error('skipping soap entry')
                                continue
                gmDispatcher.send(signal = 'clin_item_updated')
                return True