Gnumed.business.gmIncomingData API documentation
Description: Handling of <INCOMING> area.

# Module `Gnumed.business.gmIncomingData`

Handling of area.

Expand source code

    # -*- coding: utf-8 -*-
    """Handling of <INCOMING> area."""
    #============================================================
    __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
    __license__ = "GPL v2 or later"

    import sys
    import os
    import logging

    if __name__ == '__main__':
            sys.path.insert(0, '../../')

    from Gnumed.pycommon import gmI18N
    if __name__ == '__main__':
            gmI18N.activate_locale()
            gmI18N.install_domain()
    from Gnumed.pycommon import gmTools
    from Gnumed.pycommon import gmBusinessDBObject
    from Gnumed.pycommon import gmPG2
    from Gnumed.pycommon import gmDateTime

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

    #============================================================
    # class to handle unmatched incoming clinical data
    #------------------------------------------------------------
    _SQL_get_incoming_data = """SELECT * FROM clin.v_incoming_data_unmatched WHERE %s"""

    class cIncomingData(gmBusinessDBObject.cBusinessDBObject):
            """Represents items of incoming data, say, HL7 snippets."""

            _cmd_fetch_payload = _SQL_get_incoming_data % "pk_incoming_data_unmatched = %s"
            _cmds_store_payload = [
                    """UPDATE clin.incoming_data_unmatched SET
                                    fk_patient_candidates = %(pk_patient_candidates)s,
                                    fk_identity_disambiguated = %(pk_identity_disambiguated)s,
                                    fk_provider_disambiguated = %(pk_provider_disambiguated)s,
                                    request_id = gm.nullify_empty_string(%(request_id)s),
                                    firstnames = gm.nullify_empty_string(%(firstnames)s),
                                    lastnames = gm.nullify_empty_string(%(lastnames)s),
                                    dob = %(dob)s,
                                    postcode = gm.nullify_empty_string(%(postcode)s),
                                    other_info = gm.nullify_empty_string(%(other_info)s),
                                    type = gm.nullify_empty_string(%(data_type)s),
                                    gender = gm.nullify_empty_string(%(gender)s),
                                    requestor = gm.nullify_empty_string(%(requestor)s),
                                    external_data_id = gm.nullify_empty_string(%(external_data_id)s),
                                    comment = gm.nullify_empty_string(%(comment)s)
                            WHERE
                                    pk = %(pk_incoming_data_unmatched)s
                                            AND
                                    xmin = %(xmin_incoming_data_unmatched)s
                            RETURNING
                                    xmin as xmin_incoming_data_unmatched,
                                    octet_length(data) as data_size
                    """
            ]
            # view columns that can be updated:
            _updatable_fields = [
                    'pk_patient_candidates',
                    'request_id',                                           # request ID as found in <data>
                    'firstnames',
                    'lastnames',
                    'dob',
                    'postcode',
                    'other_info',                                           # other identifying info in .data
                    'data_type',
                    'gender',
                    'requestor',                                            # Requestor of data (e.g. who ordered test results) if available in source data.
                    'external_data_id',                             # ID of content of .data in external system (e.g. importer) where appropriate
                    'comment',                                                      # a free text comment on this row, eg. why is it here, error logs etc
                    'pk_identity_disambiguated',
                    'pk_provider_disambiguated'             # The provider the data is relevant to.
            ]
            #--------------------------------------------------------
            def format(self):
                    return '%s' % self
            #--------------------------------------------------------
            def _format_patient_identification(self):
                    tmp = '%s %s %s' % (
                            gmTools.coalesce(self._payload[self._idx['lastnames']], '', 'last=%s'),
                            gmTools.coalesce(self._payload[self._idx['firstnames']], '', 'first=%s'),
                            gmTools.coalesce(self._payload[self._idx['gender']], '', 'gender=%s')
                    )
                    if self._payload[self._idx['dob']] is not None:
                            tmp += ' dob=%s' % gmDateTime.pydt_strftime(self._payload[self._idx['dob']], '%Y %b %d')
                    return tmp

            patient_identification = property(_format_patient_identification, lambda x:x)

            #--------------------------------------------------------
            def update_data_from_file(self, fname=None):
                    # sanity check
                    if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                            _log.error('[%s] is not a readable file' % fname)
                            return False

                    _log.debug('updating [pk=%s] from [%s]', self.pk_obj, fname)
                    gmPG2.file2bytea (
                            query = "UPDATE clin.incoming_data_unmatched SET data = %(data)s::bytea WHERE pk = %(pk)s",
                            filename = fname,
                            args = {'pk': self.pk_obj}
                    )

                    # must update XMIN now ...
                    self.refetch_payload()
                    return True

            #--------------------------------------------------------
            def save_to_file(self, aChunkSize=0, filename=None):

                    if self._payload[self._idx['data_size']] == 0:
                            return None

                    if self._payload[self._idx['data_size']] is None:
                            return None

                    if filename is None:
                            filename = gmTools.get_unique_filename(prefix = 'gm-incoming_data_unmatched-')

                    success = gmPG2.bytea2file (
                            data_query = {
                                    'cmd': 'SELECT substring(data from %(start)s for %(size)s) FROM clin.incoming_data_unmatched WHERE pk = %(pk)s',
                                    'args': {'pk': self.pk_obj}
                            },
                            filename = filename,
                            chunk_size = aChunkSize,
                            data_size = self._payload[self._idx['data_size']]
                    )

                    if not success:
                            return None

                    return filename

            #--------------------------------------------------------
            def lock(self, exclusive=False):
                    return gmPG2.lock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

            #--------------------------------------------------------
            def unlock(self, exclusive=False):
                    return gmPG2.unlock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

    #------------------------------------------------------------
    def get_incoming_data(order_by=None, return_pks=False):
            if order_by is None:
                    order_by = 'true'
            else:
                    order_by = 'true ORDER BY %s' % order_by
            cmd = _SQL_get_incoming_data % order_by
            rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = True)
            if return_pks:
                    return [ r['pk_incoming_data_unmatched'] for r in rows ]
            return [ cIncomingData(row = {'data': r, 'idx': idx, 'pk_field': 'pk_incoming_data_unmatched'}) for r in rows ]

    #------------------------------------------------------------
    def create_incoming_data(data_type, filename):
            args = {'typ': data_type}
            cmd = """
                    INSERT INTO clin.incoming_data_unmatched (type, data)
                    VALUES (%(typ)s, 'new data'::bytea)
                    RETURNING pk"""
            rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
            pk = rows[0]['pk']
            incoming = cIncomingData(aPK_obj = pk)
            if not incoming.update_data_from_file(fname = filename):
                    _log.debug('cannot update newly created incoming_data record from file, deleting stub')
                    delete_incoming_data(incoming_data = pk)
                    return None
            return incoming

    #------------------------------------------------------------
    def delete_incoming_data(pk_incoming_data=None):
            args = {'pk': pk_incoming_data}
            cmd = "DELETE FROM clin.incoming_data_unmatched WHERE pk = %(pk)s"
            gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
            return True

    #============================================================
    # main
    #------------------------------------------------------------
    if __name__ == "__main__":

            if len(sys.argv) < 2:
                    sys.exit()

            if sys.argv[1] != 'test':
                    sys.exit()

            from Gnumed.pycommon import gmLog2

            gmDateTime.init()
            gmTools.gmPaths()

            #-------------------------------------------------------
            def test_incoming_data():
                    for d in get_incoming_data():
                            print(d)

            #-------------------------------------------------------
            test_incoming_data()

## Functions

`def create_incoming_data(data_type, filename)`
  Expand source code

      def create_incoming_data(data_type, filename):
              args = {'typ': data_type}
              cmd = """
                      INSERT INTO clin.incoming_data_unmatched (type, data)
                      VALUES (%(typ)s, 'new data'::bytea)
                      RETURNING pk"""
              rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
              pk = rows[0]['pk']
              incoming = cIncomingData(aPK_obj = pk)
              if not incoming.update_data_from_file(fname = filename):
                      _log.debug('cannot update newly created incoming_data record from file, deleting stub')
                      delete_incoming_data(incoming_data = pk)
                      return None
              return incoming

`def delete_incoming_data(pk_incoming_data=None)`
  Expand source code

      def delete_incoming_data(pk_incoming_data=None):
              args = {'pk': pk_incoming_data}
              cmd = "DELETE FROM clin.incoming_data_unmatched WHERE pk = %(pk)s"
              gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
              return True

`def get_incoming_data(order_by=None, return_pks=False)`
  Expand source code

      def get_incoming_data(order_by=None, return_pks=False):
              if order_by is None:
                      order_by = 'true'
              else:
                      order_by = 'true ORDER BY %s' % order_by
              cmd = _SQL_get_incoming_data % order_by
              rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = True)
              if return_pks:
                      return [ r['pk_incoming_data_unmatched'] for r in rows ]
              return [ cIncomingData(row = {'data': r, 'idx': idx, 'pk_field': 'pk_incoming_data_unmatched'}) for r in rows ]

## Classes

`class cIncomingData (aPK_obj=None, row: dict = None, link_obj=None)`

  Represents items of incoming data, say, HL7 snippets.

  Init business object.

  Call from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend * a simple value the primary key WHERE condition must be a simple column * a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
  `row`
    must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs

  ## Examples

  row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]

  Expand source code

      class cIncomingData(gmBusinessDBObject.cBusinessDBObject):
              """Represents items of incoming data, say, HL7 snippets."""

              _cmd_fetch_payload = _SQL_get_incoming_data % "pk_incoming_data_unmatched = %s"
              _cmds_store_payload = [
                      """UPDATE clin.incoming_data_unmatched SET
                                      fk_patient_candidates = %(pk_patient_candidates)s,
                                      fk_identity_disambiguated = %(pk_identity_disambiguated)s,
                                      fk_provider_disambiguated = %(pk_provider_disambiguated)s,
                                      request_id = gm.nullify_empty_string(%(request_id)s),
                                      firstnames = gm.nullify_empty_string(%(firstnames)s),
                                      lastnames = gm.nullify_empty_string(%(lastnames)s),
                                      dob = %(dob)s,
                                      postcode = gm.nullify_empty_string(%(postcode)s),
                                      other_info = gm.nullify_empty_string(%(other_info)s),
                                      type = gm.nullify_empty_string(%(data_type)s),
                                      gender = gm.nullify_empty_string(%(gender)s),
                                      requestor = gm.nullify_empty_string(%(requestor)s),
                                      external_data_id = gm.nullify_empty_string(%(external_data_id)s),
                                      comment = gm.nullify_empty_string(%(comment)s)
                              WHERE
                                      pk = %(pk_incoming_data_unmatched)s
                                              AND
                                      xmin = %(xmin_incoming_data_unmatched)s
                              RETURNING
                                      xmin as xmin_incoming_data_unmatched,
                                      octet_length(data) as data_size
                      """
              ]
              # view columns that can be updated:
              _updatable_fields = [
                      'pk_patient_candidates',
                      'request_id',                                           # request ID as found in <data>
                      'firstnames',
                      'lastnames',
                      'dob',
                      'postcode',
                      'other_info',                                           # other identifying info in .data
                      'data_type',
                      'gender',
                      'requestor',                                            # Requestor of data (e.g. who ordered test results) if available in source data.
                      'external_data_id',                             # ID of content of .data in external system (e.g. importer) where appropriate
                      'comment',                                                      # a free text comment on this row, eg. why is it here, error logs etc
                      'pk_identity_disambiguated',
                      'pk_provider_disambiguated'             # The provider the data is relevant to.
              ]
              #--------------------------------------------------------
              def format(self):
                      return '%s' % self
              #--------------------------------------------------------
              def _format_patient_identification(self):
                      tmp = '%s %s %s' % (
                              gmTools.coalesce(self._payload[self._idx['lastnames']], '', 'last=%s'),
                              gmTools.coalesce(self._payload[self._idx['firstnames']], '', 'first=%s'),
                              gmTools.coalesce(self._payload[self._idx['gender']], '', 'gender=%s')
                      )
                      if self._payload[self._idx['dob']] is not None:
                              tmp += ' dob=%s' % gmDateTime.pydt_strftime(self._payload[self._idx['dob']], '%Y %b %d')
                      return tmp

              patient_identification = property(_format_patient_identification, lambda x:x)

              #--------------------------------------------------------
              def update_data_from_file(self, fname=None):
                      # sanity check
                      if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                              _log.error('[%s] is not a readable file' % fname)
                              return False

                      _log.debug('updating [pk=%s] from [%s]', self.pk_obj, fname)
                      gmPG2.file2bytea (
                              query = "UPDATE clin.incoming_data_unmatched SET data = %(data)s::bytea WHERE pk = %(pk)s",
                              filename = fname,
                              args = {'pk': self.pk_obj}
                      )

                      # must update XMIN now ...
                      self.refetch_payload()
                      return True

              #--------------------------------------------------------
              def save_to_file(self, aChunkSize=0, filename=None):

                      if self._payload[self._idx['data_size']] == 0:
                              return None

                      if self._payload[self._idx['data_size']] is None:
                              return None

                      if filename is None:
                              filename = gmTools.get_unique_filename(prefix = 'gm-incoming_data_unmatched-')

                      success = gmPG2.bytea2file (
                              data_query = {
                                      'cmd': 'SELECT substring(data from %(start)s for %(size)s) FROM clin.incoming_data_unmatched WHERE pk = %(pk)s',
                                      'args': {'pk': self.pk_obj}
                              },
                              filename = filename,
                              chunk_size = aChunkSize,
                              data_size = self._payload[self._idx['data_size']]
                      )

                      if not success:
                              return None

                      return filename

              #--------------------------------------------------------
              def lock(self, exclusive=False):
                      return gmPG2.lock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

              #--------------------------------------------------------
              def unlock(self, exclusive=False):
                      return gmPG2.unlock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `var patient_identification`
    Expand source code

        def _format_patient_identification(self):
                tmp = '%s %s %s' % (
                        gmTools.coalesce(self._payload[self._idx['lastnames']], '', 'last=%s'),
                        gmTools.coalesce(self._payload[self._idx['firstnames']], '', 'first=%s'),
                        gmTools.coalesce(self._payload[self._idx['gender']], '', 'gender=%s')
                )
                if self._payload[self._idx['dob']] is not None:
                        tmp += ' dob=%s' % gmDateTime.pydt_strftime(self._payload[self._idx['dob']], '%Y %b %d')
                return tmp

  ### Methods

  `def lock(self, exclusive=False)`
    Expand source code

        def lock(self, exclusive=False):
                return gmPG2.lock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

  `def save_to_file(self, aChunkSize=0, filename=None)`
    Expand source code

        def save_to_file(self, aChunkSize=0, filename=None):

                if self._payload[self._idx['data_size']] == 0:
                        return None

                if self._payload[self._idx['data_size']] is None:
                        return None

                if filename is None:
                        filename = gmTools.get_unique_filename(prefix = 'gm-incoming_data_unmatched-')

                success = gmPG2.bytea2file (
                        data_query = {
                                'cmd': 'SELECT substring(data from %(start)s for %(size)s) FROM clin.incoming_data_unmatched WHERE pk = %(pk)s',
                                'args': {'pk': self.pk_obj}
                        },
                        filename = filename,
                        chunk_size = aChunkSize,
                        data_size = self._payload[self._idx['data_size']]
                )

                if not success:
                        return None

                return filename

  `def unlock(self, exclusive=False)`
    Expand source code

        def unlock(self, exclusive=False):
                return gmPG2.unlock_row(table = 'clin.incoming_data_unmatched', pk = self.pk_obj, exclusive = exclusive)

  `def update_data_from_file(self, fname=None)`
    Expand source code

        def update_data_from_file(self, fname=None):
                # sanity check
                if not (os.access(fname, os.R_OK) and os.path.isfile(fname)):
                        _log.error('[%s] is not a readable file' % fname)
                        return False

                _log.debug('updating [pk=%s] from [%s]', self.pk_obj, fname)
                gmPG2.file2bytea (
                        query = "UPDATE clin.incoming_data_unmatched SET data = %(data)s::bytea WHERE pk = %(pk)s",
                        filename = fname,
                        args = {'pk': self.pk_obj}
                )

                # must update XMIN now ...
                self.refetch_payload()
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`