Gnumed.business.gmDocuments API documentation
Description: This module encapsulates a document stored in a GNUmed database.

# Module `Gnumed.business.gmDocuments`

This module encapsulates a document stored in a GNUmed database.

## Functions

`def check_mimetypes_in_archive()`
  Expand source code

      def check_mimetypes_in_archive():
              mimetypes = {}
              cmd = 'SELECT pk FROM blobs.doc_med'
              doc_pks = gmPG2.run_ro_queries(queries = [{'sql': cmd}])
              print('Detecting mimetypes in document archive ...')
              doc_idx = 0
              part_count = 0
              for pk_row in doc_pks:
                      doc_idx += 1
                      print('\n#%s - document %s of %s: ' % (pk_row['pk'], doc_idx, len(doc_pks)), end = '')
                      doc = cDocument(aPK_obj = pk_row['pk'])
                      for part in doc.parts:
                              part_count += 1
                              print('#%s:%s bytes, ' % (part['pk_obj'], part['size']), end = '')
                              part_fname = part.save_to_file()
                              mimetype = gmMimeLib.guess_mimetype(part_fname)
                              try:
                                      mimetypes[mimetype]['count'] += 1
                              except KeyError:
                                      mimetypes[mimetype] = {
                                              'count': 1,
                                              'viewer': gmMimeLib.get_viewer_cmd(mimetype),
                                              'editor': gmMimeLib.get_editor_cmd(mimetype),
                                              'extension': gmMimeLib.guess_ext_by_mimetype(mimetype)
                                      }
              print('')
              print('')
              print('Number of documents :', len(doc_pks))
              print('Number of parts     :', part_count)
              print('Number of mime types:', len(mimetypes))
              for mimetype in mimetypes:
                      print('')
                      print('<%s>' % mimetype)
                      print(' Extension:', mimetypes[mimetype]['extension'])
                      print(' Use count:', mimetypes[mimetype]['count'])
                      print('    Viewer:', mimetypes[mimetype]['viewer'])
                      print('    Editor:', mimetypes[mimetype]['editor'])
              return 0

`def create_document(document_type=None, encounter=None, episode=None, link_obj=None)`
  Expand source code

      def create_document(document_type=None, encounter=None, episode=None, link_obj=None):
              """Returns new document instance or raises an exception."""
              try:
                      int(document_type)
                      SQL = "INSERT INTO blobs.doc_med (fk_type, fk_encounter, fk_episode) VALUES (%(type)s, %(pk_enc)s, %(pk_epi)s) RETURNING pk"
              except ValueError:
                      create_document_type(document_type = document_type)
                      SQL = """
                              INSERT INTO blobs.doc_med (
                                      fk_type,
                                      fk_encounter,
                                      fk_episode
                              ) VALUES (
                                      coalesce (
                                              (SELECT pk FROM blobs.doc_type bdt WHERE bdt.name = %(type)s),
                                              (SELECT pk FROM blobs.doc_type bdt WHERE _(bdt.name) = %(type)s)
                                      ),
                                      %(pk_enc)s,
                                      %(pk_epi)s
                              ) RETURNING pk"""
              args = {'type': document_type}
              try: args['pk_enc'] = int(encounter)
              except (TypeError, ValueError): args['pk_enc'] = encounter['pk_encounter']
              try: args['pk_epi'] = int(episode)
              except (TypeError, ValueError): args['pk_epi'] = episode['pk_episode']
              rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'sql': SQL, 'args': args}], return_data = True)
              doc = cDocument(aPK_obj = rows[0][0], link_obj = link_obj)
              return doc

  Returns new document instance or raises an exception.

`def create_document_type(document_type: str = None) ‑> cDocumentType`
  Expand source code

      def create_document_type(document_type:str=None) -> cDocumentType:
              # check for potential dupes:
              SQL = 'SELECT pk FROM blobs.doc_type WHERE name = %(doc_type)s'
              args = {'doc_type': document_type}
              rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
              if rows:
                      return cDocumentType(aPK_obj = rows[0][0])

              _log.debug('creating document type [%s]', document_type)
              SQL = "INSERT INTO blobs.doc_type (name) VALUES (%(doc_type)s) RETURNING pk"
              args = {'doc_type': document_type}
              rows = gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}], return_data = True)
              return cDocumentType(aPK_obj = rows[0][0])

`def delete_document(document_id=None, encounter_id=None)`
  Expand source code

      def delete_document(document_id=None, encounter_id=None):
              # cascades to doc_obj and doc_desc but not bill.bill
              cmd = "SELECT blobs.delete_document(%(pk)s, %(enc)s)"
              args = {'pk': document_id, 'enc': encounter_id}
              rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True)
              if not rows[0][0]:
                      _log.error('cannot delete document [%s]', document_id)
                      return False
              return True

`def delete_document_part(part_pk=None, encounter_pk=None)`
  Expand source code

      def delete_document_part(part_pk=None, encounter_pk=None):
              cmd = """
                      SELECT blobs.delete_document_part(%(pk)s, %(enc)s)
                      WHERE NOT EXISTS
                              (SELECT 1 FROM clin.export_item WHERE fk_doc_obj = %(pk)s)
              """
              args = {'pk': part_pk, 'enc': encounter_pk}
              gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
              return

`def delete_document_type(document_type=None)`
  Expand source code

      def delete_document_type(document_type=None):
              if document_type['is_in_use']:
                      return False

              SQL = 'DELETE FROM blobs.doc_type WHERE pk = %(pk_doc_type)s'
              args = {'pk_doc_type': document_type['pk_doc_type']}
              gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])
              return True

`def generate_failsafe_document_list_entries(pk_patient: int = None, max_width: int = 80, eol: str = None) ‑> str | list`
  Expand source code

      def generate_failsafe_document_list_entries(pk_patient:int=None, max_width:int=80, eol:str=None) -> str|list:
              lines = []
              doc_folder = cDocumentFolder(aPKey = pk_patient)
              docs = doc_folder.get_documents(order_by = 'clin_when DESC, l10n_type')
              for doc in docs:
                      lines.append('')
                      lines.extend(doc.format_for_failsafe_output(max_width = max_width))
              if not eol:
                      return lines

              return eol.join(lines)

`def get_document_type_pk(document_type=None)`
  Expand source code

      def get_document_type_pk(document_type=None):
              args = {'typ': document_type.strip()}

              cmd = 'SELECT pk FROM blobs.doc_type WHERE name = %(typ)s'
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
              if len(rows) == 0:
                      cmd = 'SELECT pk FROM blobs.doc_type WHERE _(name) = %(typ)s'
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])

              if len(rows) == 0:
                      return None

              return rows[0]['pk']

`def get_document_types()`
  Expand source code

      def get_document_types():
              rows = gmPG2.run_ro_queries (
                      queries = [{'sql': "SELECT * FROM blobs.v_doc_type"}]
              )
              doc_types = []
              for row in rows:
                      row_def = {'pk_field': 'pk_doc_type', 'data': row}
                      doc_types.append(cDocumentType(row = row_def))
              return doc_types

`def get_ext_ref()`
  Expand source code

      def get_ext_ref():
              """This needs *considerably* more smarts."""
              dirname = gmTools.get_unique_filename (
                      prefix = '',
                      suffix = time.strftime(".%Y%m%d-%H%M%S", time.localtime())
              )
              # extract name for dir
              path, doc_ID = os.path.split(dirname)
              return doc_ID

  This needs considerably more smarts.

`def map_types2pk(document_types=None)`
  Expand source code

      def map_types2pk(document_types=None):
              args = {'types': document_types}
              cmd = 'SELECT pk_doc_type, coalesce(l10n_type, type) as desc FROM blobs.v_doc_type WHERE l10n_type = ANY(%(types)s) OR type = ANY(%(types)s)'
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
              return rows

`def reclassify_documents_by_type(original_type=None, target_type=None)`
  Expand source code

      def reclassify_documents_by_type(original_type=None, target_type=None):

              _log.debug('reclassifying documents by type')
              _log.debug('original: %s', original_type)
              _log.debug('target: %s', target_type)

              if target_type['pk_doc_type'] == original_type['pk_doc_type']:
                      return True

              cmd = """
      update blobs.doc_med set
              fk_type = %(new_type)s
      WHERE
              fk_type = %(old_type)s
      """
              args = {'new_type': target_type['pk_doc_type'], 'old_type': original_type['pk_doc_type']}

              gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])

              return True

`def search_for_documents(patient_id=None,
type_id=None,
external_reference=None,
pk_episode=None,
pk_types=None)`
  Expand source code

      def search_for_documents(patient_id=None, type_id=None, external_reference=None, pk_episode=None, pk_types=None):
              """Searches for documents with the given patient and type ID."""

              if (patient_id is None) and (pk_episode is None):
                      raise ValueError('need patient_id or pk_episode to search for document')

              where_parts = []
              args = {
                      'pat_id': patient_id,
                      'type_id': type_id,
                      'ref': external_reference,
                      'pk_epi': pk_episode
              }

              if patient_id is not None:
                      where_parts.append('pk_patient = %(pat_id)s')

              if type_id is not None:
                      where_parts.append('pk_type = %(type_id)s')

              if external_reference is not None:
                      where_parts.append('ext_ref = %(ref)s')

              if pk_episode is not None:
                      where_parts.append('pk_episode = %(pk_epi)s')

              if pk_types is not None:
                      where_parts.append('pk_type = ANY(%(pk_types)s)')
                      args['pk_types'] = pk_types

              cmd = _SQL_get_document_fields % ' AND '.join(where_parts)
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
              return [ cDocument(row = {'data': r, 'pk_field': 'pk_doc'}) for r in rows ]

  Searches for documents with the given patient and type ID.

## Classes

`class cDocument (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      class cDocument(gmBusinessDBObject.cBusinessDBObject):
              """Represents one medical document."""

              _cmd_fetch_payload = _SQL_get_document_fields % "pk_doc = %s"
              _cmds_store_payload = [
                      """UPDATE blobs.doc_med SET
                                      fk_type = %(pk_type)s,
                                      fk_episode = %(pk_episode)s,
                                      fk_encounter = %(pk_encounter)s,
                                      fk_org_unit = %(pk_org_unit)s,
                                      unit_is_receiver = %(unit_is_receiver)s,
                                      clin_when = %(clin_when)s,
                                      comment = gm.nullify_empty_string(%(comment)s),
                                      ext_ref = gm.nullify_empty_string(%(ext_ref)s),
                                      fk_hospital_stay = %(pk_hospital_stay)s
                              WHERE
                                      pk = %(pk_doc)s and
                                      xmin = %(xmin_doc_med)s
                              RETURNING
                                      xmin AS xmin_doc_med"""
              ]
              _updatable_fields = [
                      'pk_type',
                      'comment',
                      'clin_when',
                      'ext_ref',
                      'pk_episode',
                      'pk_encounter',                 # mainly useful when moving visual progress notes to their respective encounters
                      'pk_org_unit',
                      'unit_is_receiver',
                      'pk_hospital_stay'
              ]

              #--------------------------------------------------------
              def refetch_payload(self, ignore_changes=False, link_obj=None):
                      try: del self.__has_unreviewed_parts
                      except AttributeError: pass

                      return super().refetch_payload(ignore_changes = ignore_changes, link_obj = link_obj)

              #--------------------------------------------------------
              def get_descriptions(self, max_lng:int=250):
                      """Get document descriptions.

                      - will return a list of rows
                      """
                      if max_lng is None:
                              SQL = "SELECT pk, text FROM blobs.doc_desc WHERE fk_doc = %(pk_doc)s"
                      else:
                              SQL = "SELECT pk, substring(text FROM 1 for %s) FROM blobs.doc_desc WHERE fk_doc = %%(pk_doc)s" % max_lng
                      args = {'pk_doc': self.pk_obj}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      return rows

              #--------------------------------------------------------
              def add_description(self, description=None):
                      SQL = 'INSERT INTO blobs.doc_desc (fk_doc, text) values (%(pk_doc)s, %(desc)s)'
                      args = {'pk_doc': self.pk_obj, 'desc': description}
                      gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])
                      return True

              #--------------------------------------------------------
              def update_description(self, pk=None, description=None):
                      cmd = "update blobs.doc_desc set text = %(desc)s WHERE fk_doc = %(doc)s and pk = %(pk_desc)s"
                      gmPG2.run_rw_queries(queries = [
                              {'sql': cmd, 'args': {'doc': self.pk_obj, 'pk_desc': pk, 'desc': description}}
                      ])
                      return True

              #--------------------------------------------------------
              def delete_description(self, pk=None):
                      cmd = "DELETE FROM blobs.doc_desc WHERE fk_doc = %(doc)s and pk = %(desc)s"
                      gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': {'doc': self.pk_obj, 'desc': pk}}])
                      return True

              #--------------------------------------------------------
              def _get_parts(self):
                      SQL = _SQL_get_document_part_fields % 'pk_doc = %(pk_doc)s ORDER BY seq_idx'
                      args = {'pk_doc': self.pk_obj}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      return [ cDocumentPart(row = {'pk_field': 'pk_obj', 'data': r}) for r in rows ]

              parts = property(_get_parts)

              #--------------------------------------------------------
              def add_part(self, file=None, link_obj=None):
                      """Add a part to the document."""
                      # create dummy part
                      cmd = """
                              INSERT INTO blobs.doc_obj (
                                      fk_doc, data, seq_idx
                              ) VALUES (
                                      %(doc_id)s,
                                      ''::bytea,
                                      (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                              ) RETURNING pk"""
                      rows = gmPG2.run_rw_queries (
                              link_obj = link_obj,
                              queries = [{'sql': cmd, 'args': {'doc_id': self.pk_obj}}],
                              return_data = True
                      )
                      # init document part instance
                      pk_part = rows[0][0]
                      new_part = cDocumentPart(aPK_obj = pk_part, link_obj = link_obj)
                      if not new_part.update_data_from_file(link_obj = link_obj, fname = file):
                              _log.error('cannot import binary data from [%s] into document part' % file)
                              SQL = 'DELETE FROM blobs.doc_obj WHERE pk = %(pk_part)s'
                              args = {'pk_part': pk_part}
                              gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'sql': SQL, 'args': args}])
                              return None

                      new_part['filename'] = file
                      new_part.save_payload(conn = link_obj)
                      return new_part

              #--------------------------------------------------------
              def add_parts_from_files(self, files=None, reviewer=None):

                      new_parts = []

                      for filename in files:
                              new_part = self.add_part(file = filename)
                              if new_part is None:
                                      msg = 'cannot instantiate document part object from [%s]' % filename
                                      _log.error(msg)
                                      return (False, msg, filename)
                              new_parts.append(new_part)

                              if reviewer is not None:
                                      new_part['pk_intended_reviewer'] = reviewer                     # None == Null
                                      success, data = new_part.save_payload()
                                      if not success:
                                              msg = 'cannot set reviewer to [%s] on [%s]' % (reviewer, filename)
                                              _log.error(msg)
                                              _log.error(str(data))
                                              return (False, msg, filename)

                      return (True, '', new_parts)

              #--------------------------------------------------------
              def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None):
                      fnames = []
                      for part in self.parts:
                              fname = part.save_to_file(aChunkSize = chunksize, directory = export_dir, conn = conn)
                              if fname is None:
                                      _log.error('cannot export document part [%s]', part)
                                      continue
                              fnames.append(fname)
                      return fnames

              #--------------------------------------------------------
              def add_part_from_incoming(self, pk_incoming:int=None, pk_reviewer:int=None, conn=None):
                      SQL = """
                              INSERT INTO blobs.doc_obj (
                                      fk_doc, data, seq_idx
                              ) VALUES (
                                      %(doc_id)s,
                                      ''::bytea,
                                      (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                              ) RETURNING pk
                      """
                      args = {'doc_id': self.pk_obj}
                      rows = gmPG2.run_rw_queries(link_obj = conn, queries = [{'sql': SQL, 'args': args}], return_data = True)
                      new_part = cDocumentPart(aPK_obj = rows[0]['pk'], link_obj = conn)
                      if not new_part.update_data_from_incoming(conn = conn, pk_incoming = pk_incoming):
                              return None

                      if not pk_reviewer:
                              return new_part

                      new_part['pk_intended_reviewer'] = pk_reviewer
                      success, data = new_part.save(conn = conn)
                      if success:
                              return new_part

                      msg = 'cannot set reviewer to [%s] on [%s]' % (pk_reviewer, pk_incoming)
                      _log.error(msg)
                      _log.error(str(data))
                      return None

              #--------------------------------------------------------
              def add_parts_from_incoming(self, incoming_data:list=None, pk_reviewer:int=None, conn=None):
                      """Add parts to document from gmIncomingData.cIncomingData instances.

                      Returns:
                              A tuple (success state, data). On failure data is an error message. On success data is the list of new parts.
                      """
                      new_parts = []
                      for incoming in incoming_data:
                              part = self.add_part_from_incoming (
                                      pk_incoming = incoming['pk_incoming_data'],
                                      pk_reviewer = pk_reviewer,
                                      conn = conn
                              )
                              if part:
                                      new_parts.append(part)
                                      continue
                              msg = 'cannot instantiate document part from incoming [%s]' % incoming['pk_incoming_data']
                              _log.error(msg)
                              return False, msg

                      return True, new_parts

              #--------------------------------------------------------
              def _get_has_unreviewed_parts(self):
                      try:
                              return self.__has_unreviewed_parts                      # pylint: disable=access-member-before-definition

                      except AttributeError:
                              pass

                      cmd = "SELECT EXISTS(SELECT 1 FROM blobs.v_obj4doc_no_data WHERE pk_doc = %(pk)s AND reviewed IS FALSE)"
                      args = {'pk': self.pk_obj}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      self.__has_unreviewed_parts = rows[0][0]
                      return self.__has_unreviewed_parts

              has_unreviewed_parts = property(_get_has_unreviewed_parts)

              #--------------------------------------------------------
              def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                      # FIXME: this is probably inefficient
                      for part in self.parts:
                              if not part.set_reviewed(technically_abnormal, clinically_relevant):
                                      return False
                      return True

              #--------------------------------------------------------
              def set_primary_reviewer(self, reviewer=None):
                      for part in self.parts:
                              part['pk_intended_reviewer'] = reviewer
                              success, data = part.save_payload()
                              if not success:
                                      _log.error('cannot set reviewer to [%s]' % reviewer)
                                      _log.error(str(data))
                                      return False
                      return True

              #--------------------------------------------------------
              def format_single_line(self):

                      part_count = len(self._payload['seq_idx_list'])
                      if part_count == 0:
                              parts = _('no parts')
                      elif part_count == 1:
                              parts = _('1 part')
                      else:
                              parts = _('%s parts') % part_count

                      detail = ''
                      if self._payload['ext_ref'] is not None:
                              detail = self._payload['ext_ref']
                      if self._payload['unit'] is not None:
                              template = _('%s of %s')
                              if detail == '':
                                      detail = _('%s of %s') % (
                                              self._payload['unit'],
                                              self._payload['organization']
                                      )
                              else:
                                      detail += (' @ ' + template % (
                                              self._payload['unit'],
                                              self._payload['organization']
                                      ))
                      if detail != '':
                              detail = ' (%s)' % detail

                      return '%s %s (%s):%s%s' % (
                              self._payload['clin_when'].strftime('%Y %b %d'),
                              self._payload['l10n_type'],
                              parts,
                              gmTools.coalesce(self._payload['comment'], '', ' "%s"'),
                              detail
                      )

              #--------------------------------------------------------
              def format(self, single_line=False):
                      if single_line:
                              return self.format_single_line()

                      part_count = len(self._payload['seq_idx_list'])
                      if part_count == 0:
                              parts = _('no parts')
                      elif part_count == 1:
                              parts = _('1 part')
                      else:
                              parts = _('%s parts') % part_count
                      org = ''
                      if self._payload['unit'] is not None:
                              if self._payload['unit_is_receiver']:
                                      org = _(' Receiver: %s @ %s\n') % (
                                              self._payload['unit'],
                                              self._payload['organization']
                                      )
                              else:
                                      org = _(' Sender: %s @ %s\n') % (
                                              self._payload['unit'],
                                              self._payload['organization']
                                      )
                      stay = ''
                      if self._payload['pk_hospital_stay'] is not None:
                              stay = _('Hospital stay') + ': %s\n' % self.hospital_stay.format (
                                      left_margin = 0,
                                      include_procedures = False,
                                      include_docs = False,
                                      include_episode = False
                              )

                      txt = _(
                              '%s (%s)   #%s\n'
                              ' Created: %s\n'
                              ' Episode: %s\n'
                              '%s'
                              '%s'
                              '%s'
                              '%s'
                              '%s'
                      ) % (
                              self._payload['l10n_type'],
                              parts,
                              self._payload['pk_doc'],
                              self._payload['clin_when'].strftime('%Y %b %d'),
                              self._payload['episode'],
                              gmTools.coalesce(self._payload['health_issue'], '', _(' Health issue: %s\n')),
                              gmTools.coalesce(self._payload['ext_ref'], '', _(' External reference: %s\n')),
                              org,
                              stay,
                              gmTools.coalesce(self._payload['comment'], '', ' %s')
                      )

                      return txt

              #--------------------------------------------------------
              def format_for_failsafe_output(self, max_width:int=80) -> list[str]:
                      lines = [ '%s: %s' % (self._payload['clin_when'].strftime('%Y %B %d'), self._payload['l10n_type']) ]
                      if self._payload['unit'] and not self._payload['unit_is_receiver']:
                              lines.append('  ' + _('From: %s @ %s') % (self._payload['unit'], self._payload['organization']))
                      return lines

              #--------------------------------------------------------
              def _get_hospital_stay(self):
                      if self._payload['pk_hospital_stay'] is None:
                              return None

                      return gmHospitalStay.cHospitalStay(self._payload['pk_hospital_stay'])

              hospital_stay = property(_get_hospital_stay)

              #--------------------------------------------------------
              def _get_org_unit(self):
                      if self._payload['pk_org_unit'] is None:
                              return None
                      return gmOrganization.cOrgUnit(self._payload['pk_org_unit'])

              org_unit = property(_get_org_unit)

              #--------------------------------------------------------
              def _get_procedures(self):
                      from Gnumed.business.gmPerformedProcedure import get_procedures4document
                      return get_procedures4document(pk_document = self.pk_obj)

              procedures = property(_get_procedures)

              #--------------------------------------------------------
              def _get_bills(self):
                      from Gnumed.business.gmBilling import get_bills4document
                      return get_bills4document(pk_document = self.pk_obj)

              bills = property(_get_bills)

              #--------------------------------------------------------
              def __get_encounter(self):
                      return gmEncounter.cEncounter(aPK_obj = self._payload['pk_encounter'])

              encounter = property(__get_encounter)

  Represents one medical document.

  Call init from child classes like so:

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

  ## Args

  `aPK_obj`
    retrieve data from backend
  - an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
  - a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
  `row`
    must hold the fields
  - data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
  - pk_field: the name of the primary key column OR
  - pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
  - for example:

        row = {
                'data': rows[0],
                'pk_field': 'pk_XXX (the PK column name)',
                'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
        }

        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
        objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `prop bills`
    Expand source code

        def _get_bills(self):
                from Gnumed.business.gmBilling import get_bills4document
                return get_bills4document(pk_document = self.pk_obj)

  `prop encounter`
    Expand source code

        def __get_encounter(self):
                return gmEncounter.cEncounter(aPK_obj = self._payload['pk_encounter'])

  `prop has_unreviewed_parts`
    Expand source code

        def _get_has_unreviewed_parts(self):
                try:
                        return self.__has_unreviewed_parts                      # pylint: disable=access-member-before-definition

                except AttributeError:
                        pass

                cmd = "SELECT EXISTS(SELECT 1 FROM blobs.v_obj4doc_no_data WHERE pk_doc = %(pk)s AND reviewed IS FALSE)"
                args = {'pk': self.pk_obj}
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                self.__has_unreviewed_parts = rows[0][0]
                return self.__has_unreviewed_parts

  `prop hospital_stay`
    Expand source code

        def _get_hospital_stay(self):
                if self._payload['pk_hospital_stay'] is None:
                        return None

                return gmHospitalStay.cHospitalStay(self._payload['pk_hospital_stay'])

  `prop org_unit`
    Expand source code

        def _get_org_unit(self):
                if self._payload['pk_org_unit'] is None:
                        return None
                return gmOrganization.cOrgUnit(self._payload['pk_org_unit'])

  `prop parts`
    Expand source code

        def _get_parts(self):
                SQL = _SQL_get_document_part_fields % 'pk_doc = %(pk_doc)s ORDER BY seq_idx'
                args = {'pk_doc': self.pk_obj}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                return [ cDocumentPart(row = {'pk_field': 'pk_obj', 'data': r}) for r in rows ]

  `prop procedures`
    Expand source code

        def _get_procedures(self):
                from Gnumed.business.gmPerformedProcedure import get_procedures4document
                return get_procedures4document(pk_document = self.pk_obj)

  ### Methods

  `def add_description(self, description=None)`
    Expand source code

        def add_description(self, description=None):
                SQL = 'INSERT INTO blobs.doc_desc (fk_doc, text) values (%(pk_doc)s, %(desc)s)'
                args = {'pk_doc': self.pk_obj, 'desc': description}
                gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])
                return True

  `def add_part(self, file=None, link_obj=None)`
    Expand source code

        def add_part(self, file=None, link_obj=None):
                """Add a part to the document."""
                # create dummy part
                cmd = """
                        INSERT INTO blobs.doc_obj (
                                fk_doc, data, seq_idx
                        ) VALUES (
                                %(doc_id)s,
                                ''::bytea,
                                (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                        ) RETURNING pk"""
                rows = gmPG2.run_rw_queries (
                        link_obj = link_obj,
                        queries = [{'sql': cmd, 'args': {'doc_id': self.pk_obj}}],
                        return_data = True
                )
                # init document part instance
                pk_part = rows[0][0]
                new_part = cDocumentPart(aPK_obj = pk_part, link_obj = link_obj)
                if not new_part.update_data_from_file(link_obj = link_obj, fname = file):
                        _log.error('cannot import binary data from [%s] into document part' % file)
                        SQL = 'DELETE FROM blobs.doc_obj WHERE pk = %(pk_part)s'
                        args = {'pk_part': pk_part}
                        gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'sql': SQL, 'args': args}])
                        return None

                new_part['filename'] = file
                new_part.save_payload(conn = link_obj)
                return new_part

    Add a part to the document.

  `def add_part_from_incoming(self, pk_incoming: int = None, pk_reviewer: int = None, conn=None)`
    Expand source code

        def add_part_from_incoming(self, pk_incoming:int=None, pk_reviewer:int=None, conn=None):
                SQL = """
                        INSERT INTO blobs.doc_obj (
                                fk_doc, data, seq_idx
                        ) VALUES (
                                %(doc_id)s,
                                ''::bytea,
                                (SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s)
                        ) RETURNING pk
                """
                args = {'doc_id': self.pk_obj}
                rows = gmPG2.run_rw_queries(link_obj = conn, queries = [{'sql': SQL, 'args': args}], return_data = True)
                new_part = cDocumentPart(aPK_obj = rows[0]['pk'], link_obj = conn)
                if not new_part.update_data_from_incoming(conn = conn, pk_incoming = pk_incoming):
                        return None

                if not pk_reviewer:
                        return new_part

                new_part['pk_intended_reviewer'] = pk_reviewer
                success, data = new_part.save(conn = conn)
                if success:
                        return new_part

                msg = 'cannot set reviewer to [%s] on [%s]' % (pk_reviewer, pk_incoming)
                _log.error(msg)
                _log.error(str(data))
                return None

  `def add_parts_from_files(self, files=None, reviewer=None)`
    Expand source code

        def add_parts_from_files(self, files=None, reviewer=None):

                new_parts = []

                for filename in files:
                        new_part = self.add_part(file = filename)
                        if new_part is None:
                                msg = 'cannot instantiate document part object from [%s]' % filename
                                _log.error(msg)
                                return (False, msg, filename)
                        new_parts.append(new_part)

                        if reviewer is not None:
                                new_part['pk_intended_reviewer'] = reviewer                     # None == Null
                                success, data = new_part.save_payload()
                                if not success:
                                        msg = 'cannot set reviewer to [%s] on [%s]' % (reviewer, filename)
                                        _log.error(msg)
                                        _log.error(str(data))
                                        return (False, msg, filename)

                return (True, '', new_parts)

  `def add_parts_from_incoming(self, incoming_data: list = None, pk_reviewer: int = None, conn=None)`
    Expand source code

        def add_parts_from_incoming(self, incoming_data:list=None, pk_reviewer:int=None, conn=None):
                """Add parts to document from gmIncomingData.cIncomingData instances.

                Returns:
                        A tuple (success state, data). On failure data is an error message. On success data is the list of new parts.
                """
                new_parts = []
                for incoming in incoming_data:
                        part = self.add_part_from_incoming (
                                pk_incoming = incoming['pk_incoming_data'],
                                pk_reviewer = pk_reviewer,
                                conn = conn
                        )
                        if part:
                                new_parts.append(part)
                                continue
                        msg = 'cannot instantiate document part from incoming [%s]' % incoming['pk_incoming_data']
                        _log.error(msg)
                        return False, msg

                return True, new_parts

    Add parts to document from gmIncomingData.cIncomingData instances.

    ## Returns

    A tuple (success state, data). On failure data is an error message. On success data is the list of new parts.

  `def delete_description(self, pk=None)`
    Expand source code

        def delete_description(self, pk=None):
                cmd = "DELETE FROM blobs.doc_desc WHERE fk_doc = %(doc)s and pk = %(desc)s"
                gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': {'doc': self.pk_obj, 'desc': pk}}])
                return True

  `def format_for_failsafe_output(self, max_width: int = 80) ‑> list[str]`
    Expand source code

        def format_for_failsafe_output(self, max_width:int=80) -> list[str]:
                lines = [ '%s: %s' % (self._payload['clin_when'].strftime('%Y %B %d'), self._payload['l10n_type']) ]
                if self._payload['unit'] and not self._payload['unit_is_receiver']:
                        lines.append('  ' + _('From: %s @ %s') % (self._payload['unit'], self._payload['organization']))
                return lines

  `def format_single_line(self)`
    Expand source code

        def format_single_line(self):

                part_count = len(self._payload['seq_idx_list'])
                if part_count == 0:
                        parts = _('no parts')
                elif part_count == 1:
                        parts = _('1 part')
                else:
                        parts = _('%s parts') % part_count

                detail = ''
                if self._payload['ext_ref'] is not None:
                        detail = self._payload['ext_ref']
                if self._payload['unit'] is not None:
                        template = _('%s of %s')
                        if detail == '':
                                detail = _('%s of %s') % (
                                        self._payload['unit'],
                                        self._payload['organization']
                                )
                        else:
                                detail += (' @ ' + template % (
                                        self._payload['unit'],
                                        self._payload['organization']
                                ))
                if detail != '':
                        detail = ' (%s)' % detail

                return '%s %s (%s):%s%s' % (
                        self._payload['clin_when'].strftime('%Y %b %d'),
                        self._payload['l10n_type'],
                        parts,
                        gmTools.coalesce(self._payload['comment'], '', ' "%s"'),
                        detail
                )

  `def get_descriptions(self, max_lng: int = 250)`
    Expand source code

        def get_descriptions(self, max_lng:int=250):
                """Get document descriptions.

                - will return a list of rows
                """
                if max_lng is None:
                        SQL = "SELECT pk, text FROM blobs.doc_desc WHERE fk_doc = %(pk_doc)s"
                else:
                        SQL = "SELECT pk, substring(text FROM 1 for %s) FROM blobs.doc_desc WHERE fk_doc = %%(pk_doc)s" % max_lng
                args = {'pk_doc': self.pk_obj}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                return rows

    Get document descriptions.

    - will return a list of rows
  `def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None)`
    Expand source code

        def save_parts_to_files(self, export_dir=None, chunksize=0, conn=None):
                fnames = []
                for part in self.parts:
                        fname = part.save_to_file(aChunkSize = chunksize, directory = export_dir, conn = conn)
                        if fname is None:
                                _log.error('cannot export document part [%s]', part)
                                continue
                        fnames.append(fname)
                return fnames

  `def set_primary_reviewer(self, reviewer=None)`
    Expand source code

        def set_primary_reviewer(self, reviewer=None):
                for part in self.parts:
                        part['pk_intended_reviewer'] = reviewer
                        success, data = part.save_payload()
                        if not success:
                                _log.error('cannot set reviewer to [%s]' % reviewer)
                                _log.error(str(data))
                                return False
                return True

  `def set_reviewed(self, technically_abnormal=None, clinically_relevant=None)`
    Expand source code

        def set_reviewed(self, technically_abnormal=None, clinically_relevant=None):
                # FIXME: this is probably inefficient
                for part in self.parts:
                        if not part.set_reviewed(technically_abnormal, clinically_relevant):
                                return False
                return True

  `def update_description(self, pk=None, description=None)`
    Expand source code

        def update_description(self, pk=None, description=None):
                cmd = "update blobs.doc_desc set text = %(desc)s WHERE fk_doc = %(doc)s and pk = %(pk_desc)s"
                gmPG2.run_rw_queries(queries = [
                        {'sql': cmd, 'args': {'doc': self.pk_obj, 'pk_desc': pk, 'desc': description}}
                ])
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cDocumentFolder (aPKey=None)`
  Expand source code

      class cDocumentFolder:
              """Represents a folder with medical documents for a single patient."""

              def __init__(self, aPKey = None):
                      """Fails if

                      - patient referenced by aPKey does not exist
                      """
                      self.pk_patient = aPKey                 # == identity.pk == primary key
                      if not self._pkey_exists():
                              raise gmExceptions.ConstructorError("No patient with PK [%s] in database." % aPKey)

                      # register backend notification interests
                      # (keep this last so we won't hang on threads when
                      #  failing this constructor for other reasons ...)
      #               if not self._register_interests():
      #                       raise gmExceptions.ConstructorError, "cannot register signal interests"

                      _log.debug('instantiated document folder for patient [%s]' % self.pk_patient)
              #--------------------------------------------------------
              def cleanup(self):
                      pass
              #--------------------------------------------------------
              # internal helper
              #--------------------------------------------------------
              def _pkey_exists(self) -> bool:
                      """Does this primary key (= patient) exist ?

                      - true/false/None
                      """
                      # patient in demographic database ?
                      SQL = 'SELECT exists(SELECT 1 FROM dem.identity WHERE pk = %(pk_pat)s)'
                      args = {'pk_pat': self.pk_patient}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      if not rows[0][0]:
                              _log.error("patient [%s] not in demographic database" % self.pk_patient)
                              return None

                      return True

              #--------------------------------------------------------
              # API
              #--------------------------------------------------------
              def get_latest_freediams_prescription(self):
                      cmd = """
                              SELECT pk_doc
                              FROM blobs.v_doc_med
                              WHERE
                                      pk_patient = %(pat)s
                                              AND
                                      type = %(typ)s
                                              AND
                                      ext_ref = %(ref)s
                              ORDER BY
                                      clin_when DESC
                              LIMIT 1
                      """
                      args = {
                              'pat': self.pk_patient,
                              'typ': DOCUMENT_TYPE_PRESCRIPTION,
                              'ref': 'FreeDiams'
                      }
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      if len(rows) == 0:
                              _log.info('no FreeDiams prescription available for patient [%s]' % self.pk_patient)
                              return None
                      prescription = cDocument(aPK_obj = rows[0][0])
                      return prescription

              #--------------------------------------------------------
              def get_latest_mugshot(self):
                      SQL = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %(pk_pat)s"
                      args = {'pk_pat': self.pk_patient}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      if rows:
                              return cDocumentPart(aPK_obj = rows[0][0])

                      _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                      return None

              latest_mugshot = property(get_latest_mugshot)

              #--------------------------------------------------------
              def get_mugshot_list(self, latest_only=True):
                      if latest_only:
                              SQL = "SELECT pk_doc, pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %(pk_pat)s"
                      else:
                              SQL = """
                                      SELECT
                                              vdm.pk_doc as pk_doc,
                                              dobj.pk as pk_obj
                                      FROM
                                              blobs.v_doc_med vdm
                                              blobs.doc_obj dobj
                                      WHERE
                                              vdm.pk_type = (SELECT pk FROM blobs.doc_type WHERE name = 'patient photograph')
                                              and vdm.pk_patient = %(pk_pat)s
                                              and dobj.fk_doc = vdm.pk_doc
                              """
                      args = {'pk_pat': self.pk_patient}
                      rows = gmPG2.run_ro_queries(queries = [{'SQL': SQL, 'args': args}])
                      return rows

              #--------------------------------------------------------
              def get_doc_list(self, doc_type=None):
                      """return flat list of document IDs"""

                      args = {
                              'ID': self.pk_patient,
                              'TYP': doc_type
                      }

                      cmd = """
                              SELECT vdm.pk_doc
                              FROM blobs.v_doc_med vdm
                              WHERE
                                      vdm.pk_patient = %%(ID)s
                                      %s
                              order by vdm.clin_when"""

                      if doc_type is None:
                              cmd = cmd % ''
                      else:
                              try:
                                      int(doc_type)
                                      cmd = cmd % 'and vdm.pk_type = %(TYP)s'
                              except (TypeError, ValueError):
                                      cmd = cmd % 'and vdm.pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(TYP)s)'

                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      doc_ids = []
                      for row in rows:
                              doc_ids.append(row[0])
                      return doc_ids

              #--------------------------------------------------------
              def get_visual_progress_notes(self, episodes=None, encounter=None):
                      return self.get_documents (
                              doc_type = DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
                              pk_episodes = episodes,
                              encounter = encounter
                      )

              #--------------------------------------------------------
              def get_unsigned_documents(self):
                      args = {'pat': self.pk_patient}
                      cmd = _SQL_get_document_fields % """
                              pk_doc = ANY (
                                      SELECT DISTINCT ON (b_vo.pk_doc) b_vo.pk_doc
                                      FROM blobs.v_obj4doc_no_data b_vo
                                      WHERE
                                              pk_patient = %(pat)s
                                                      AND
                                              reviewed IS FALSE
                              )
                              ORDER BY clin_when DESC"""
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      return [ cDocument(row = {'pk_field': 'pk_doc', 'data': r}) for r in rows ]

              #--------------------------------------------------------
              def get_documents(self, doc_type:str|int=None, pk_episodes:list[int]=None, encounter:int=None, order_by:str=None, exclude_unsigned:bool=False, pk_types:list[int]=None) -> list[cDocument]:
                      """Return list of documents."""
                      args = {
                              'pat': self.pk_patient,
                              'type': doc_type,
                              'enc': encounter
                      }
                      where_parts = ['pk_patient = %(pat)s']
                      if doc_type is not None:
                              try:
                                      int(doc_type)
                                      where_parts.append('pk_type = %(type)s')
                              except (TypeError, ValueError):
                                      where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')
                      if pk_types:
                              where_parts.append('pk_type = ANY(%(pk_types)s)')
                              args['pk_types'] = pk_types
                      if pk_episodes:
                              where_parts.append('pk_episode = ANY(%(epis)s)')
                              args['epis'] = pk_episodes
                      if encounter is not None:
                              where_parts.append('pk_encounter = %(enc)s')
                      if exclude_unsigned:
                              where_parts.append('pk_doc = ANY(SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')
                      if not order_by:
                              order_by = 'clin_when'
                      order_by_clause = 'ORDER BY %s' % order_by
                      cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by_clause)
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      return [ cDocument(row = {'pk_field': 'pk_doc', 'data': r}) for r in rows ]

              documents = property(get_documents)

              #--------------------------------------------------------
              def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None):
                      return create_document(link_obj = link_obj, document_type = document_type, encounter = encounter, episode = episode)

              #--------------------------------------------------------
              def add_prescription(self, encounter=None, episode=None, link_obj=None):
                      return self.add_document (
                              link_obj = link_obj,
                              document_type = create_document_type (
                                      document_type = DOCUMENT_TYPE_PRESCRIPTION
                              )['pk_doc_type'],
                              encounter = encounter,
                              episode = episode
                      )

              #--------------------------------------------------------
              def _get_all_document_org_units(self):
                      cmd = gmOrganization._SQL_get_org_unit % (
                              'pk_org_unit IN (SELECT DISTINCT ON (pk_org_unit) pk_org_unit FROM blobs.v_doc_med WHERE pk_patient = %(pat)s)'
                      )
                      args = {'pat': self.pk_patient}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      return [ gmOrganization.cOrgUnit(row = {'data': r, 'pk_field': 'pk_org_unit'}) for r in rows ]

              all_document_org_units = property(_get_all_document_org_units)

  Represents a folder with medical documents for a single patient.

  Fails if

  - patient referenced by aPKey does not exist

  ### Instance variables

  `prop all_document_org_units`
    Expand source code

        def _get_all_document_org_units(self):
                cmd = gmOrganization._SQL_get_org_unit % (
                        'pk_org_unit IN (SELECT DISTINCT ON (pk_org_unit) pk_org_unit FROM blobs.v_doc_med WHERE pk_patient = %(pat)s)'
                )
                args = {'pat': self.pk_patient}
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return [ gmOrganization.cOrgUnit(row = {'data': r, 'pk_field': 'pk_org_unit'}) for r in rows ]

  `prop documents : list[cDocument]`
    Expand source code

        def get_documents(self, doc_type:str|int=None, pk_episodes:list[int]=None, encounter:int=None, order_by:str=None, exclude_unsigned:bool=False, pk_types:list[int]=None) -> list[cDocument]:
                """Return list of documents."""
                args = {
                        'pat': self.pk_patient,
                        'type': doc_type,
                        'enc': encounter
                }
                where_parts = ['pk_patient = %(pat)s']
                if doc_type is not None:
                        try:
                                int(doc_type)
                                where_parts.append('pk_type = %(type)s')
                        except (TypeError, ValueError):
                                where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')
                if pk_types:
                        where_parts.append('pk_type = ANY(%(pk_types)s)')
                        args['pk_types'] = pk_types
                if pk_episodes:
                        where_parts.append('pk_episode = ANY(%(epis)s)')
                        args['epis'] = pk_episodes
                if encounter is not None:
                        where_parts.append('pk_encounter = %(enc)s')
                if exclude_unsigned:
                        where_parts.append('pk_doc = ANY(SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')
                if not order_by:
                        order_by = 'clin_when'
                order_by_clause = 'ORDER BY %s' % order_by
                cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by_clause)
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return [ cDocument(row = {'pk_field': 'pk_doc', 'data': r}) for r in rows ]

    Return list of documents.

  `prop latest_mugshot`
    Expand source code

        def get_latest_mugshot(self):
                SQL = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %(pk_pat)s"
                args = {'pk_pat': self.pk_patient}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                if rows:
                        return cDocumentPart(aPK_obj = rows[0][0])

                _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                return None

  ### Methods

  `def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None)`
    Expand source code

        def add_document(self, document_type=None, encounter=None, episode=None, link_obj=None):
                return create_document(link_obj = link_obj, document_type = document_type, encounter = encounter, episode = episode)

  `def add_prescription(self, encounter=None, episode=None, link_obj=None)`
    Expand source code

        def add_prescription(self, encounter=None, episode=None, link_obj=None):
                return self.add_document (
                        link_obj = link_obj,
                        document_type = create_document_type (
                                document_type = DOCUMENT_TYPE_PRESCRIPTION
                        )['pk_doc_type'],
                        encounter = encounter,
                        episode = episode
                )

  `def cleanup(self)`
    Expand source code

        def cleanup(self):
                pass

  `def get_doc_list(self, doc_type=None)`
    Expand source code

        def get_doc_list(self, doc_type=None):
                """return flat list of document IDs"""

                args = {
                        'ID': self.pk_patient,
                        'TYP': doc_type
                }

                cmd = """
                        SELECT vdm.pk_doc
                        FROM blobs.v_doc_med vdm
                        WHERE
                                vdm.pk_patient = %%(ID)s
                                %s
                        order by vdm.clin_when"""

                if doc_type is None:
                        cmd = cmd % ''
                else:
                        try:
                                int(doc_type)
                                cmd = cmd % 'and vdm.pk_type = %(TYP)s'
                        except (TypeError, ValueError):
                                cmd = cmd % 'and vdm.pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(TYP)s)'

                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                doc_ids = []
                for row in rows:
                        doc_ids.append(row[0])
                return doc_ids

    return flat list of document IDs

  `def get_documents(self,
  doc_type: str | int = None,
  pk_episodes: list[int] = None,
  encounter: int = None,
  order_by: str = None,
  exclude_unsigned: bool = False,
  pk_types: list[int] = None) ‑> list[cDocument]`
    Expand source code

        def get_documents(self, doc_type:str|int=None, pk_episodes:list[int]=None, encounter:int=None, order_by:str=None, exclude_unsigned:bool=False, pk_types:list[int]=None) -> list[cDocument]:
                """Return list of documents."""
                args = {
                        'pat': self.pk_patient,
                        'type': doc_type,
                        'enc': encounter
                }
                where_parts = ['pk_patient = %(pat)s']
                if doc_type is not None:
                        try:
                                int(doc_type)
                                where_parts.append('pk_type = %(type)s')
                        except (TypeError, ValueError):
                                where_parts.append('pk_type = (SELECT pk FROM blobs.doc_type WHERE name = %(type)s)')
                if pk_types:
                        where_parts.append('pk_type = ANY(%(pk_types)s)')
                        args['pk_types'] = pk_types
                if pk_episodes:
                        where_parts.append('pk_episode = ANY(%(epis)s)')
                        args['epis'] = pk_episodes
                if encounter is not None:
                        where_parts.append('pk_encounter = %(enc)s')
                if exclude_unsigned:
                        where_parts.append('pk_doc = ANY(SELECT b_vo.pk_doc FROM blobs.v_obj4doc_no_data b_vo WHERE b_vo.pk_patient = %(pat)s AND b_vo.reviewed IS TRUE)')
                if not order_by:
                        order_by = 'clin_when'
                order_by_clause = 'ORDER BY %s' % order_by
                cmd = "%s\n%s" % (_SQL_get_document_fields % ' AND '.join(where_parts), order_by_clause)
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return [ cDocument(row = {'pk_field': 'pk_doc', 'data': r}) for r in rows ]

    Return list of documents.

  `def get_latest_freediams_prescription(self)`
    Expand source code

        def get_latest_freediams_prescription(self):
                cmd = """
                        SELECT pk_doc
                        FROM blobs.v_doc_med
                        WHERE
                                pk_patient = %(pat)s
                                        AND
                                type = %(typ)s
                                        AND
                                ext_ref = %(ref)s
                        ORDER BY
                                clin_when DESC
                        LIMIT 1
                """
                args = {
                        'pat': self.pk_patient,
                        'typ': DOCUMENT_TYPE_PRESCRIPTION,
                        'ref': 'FreeDiams'
                }
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                if len(rows) == 0:
                        _log.info('no FreeDiams prescription available for patient [%s]' % self.pk_patient)
                        return None
                prescription = cDocument(aPK_obj = rows[0][0])
                return prescription

  `def get_latest_mugshot(self)`
    Expand source code

        def get_latest_mugshot(self):
                SQL = "SELECT pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %(pk_pat)s"
                args = {'pk_pat': self.pk_patient}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                if rows:
                        return cDocumentPart(aPK_obj = rows[0][0])

                _log.info('no mugshots available for patient [%s]' % self.pk_patient)
                return None

  `def get_mugshot_list(self, latest_only=True)`
    Expand source code

        def get_mugshot_list(self, latest_only=True):
                if latest_only:
                        SQL = "SELECT pk_doc, pk_obj FROM blobs.v_latest_mugshot WHERE pk_patient = %(pk_pat)s"
                else:
                        SQL = """
                                SELECT
                                        vdm.pk_doc as pk_doc,
                                        dobj.pk as pk_obj
                                FROM
                                        blobs.v_doc_med vdm
                                        blobs.doc_obj dobj
                                WHERE
                                        vdm.pk_type = (SELECT pk FROM blobs.doc_type WHERE name = 'patient photograph')
                                        and vdm.pk_patient = %(pk_pat)s
                                        and dobj.fk_doc = vdm.pk_doc
                        """
                args = {'pk_pat': self.pk_patient}
                rows = gmPG2.run_ro_queries(queries = [{'SQL': SQL, 'args': args}])
                return rows

  `def get_unsigned_documents(self)`
    Expand source code

        def get_unsigned_documents(self):
                args = {'pat': self.pk_patient}
                cmd = _SQL_get_document_fields % """
                        pk_doc = ANY (
                                SELECT DISTINCT ON (b_vo.pk_doc) b_vo.pk_doc
                                FROM blobs.v_obj4doc_no_data b_vo
                                WHERE
                                        pk_patient = %(pat)s
                                                AND
                                        reviewed IS FALSE
                        )
                        ORDER BY clin_when DESC"""
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return [ cDocument(row = {'pk_field': 'pk_doc', 'data': r}) for r in rows ]

  `def get_visual_progress_notes(self, episodes=None, encounter=None)`
    Expand source code

        def get_visual_progress_notes(self, episodes=None, encounter=None):
                return self.get_documents (
                        doc_type = DOCUMENT_TYPE_VISUAL_PROGRESS_NOTE,
                        pk_episodes = episodes,
                        encounter = encounter
                )

`class cDocumentPart (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      class cDocumentPart(gmBusinessDBObject.cBusinessDBObject):
              """Represents one part of a medical document."""

              _cmd_fetch_payload = _SQL_get_document_part_fields % "pk_obj = %s"
              _cmds_store_payload = [
                      """UPDATE blobs.doc_obj SET
                                      seq_idx = %(seq_idx)s,
                                      comment = gm.nullify_empty_string(%(obj_comment)s),
                                      filename = gm.nullify_empty_string(%(filename)s),
                                      fk_intended_reviewer = %(pk_intended_reviewer)s
                              WHERE
                                      pk = %(pk_obj)s
                                              AND
                                      xmin = %(xmin_doc_obj)s
                              RETURNING
                                      xmin AS xmin_doc_obj"""
              ]
              _updatable_fields = [
                      'seq_idx',
                      'obj_comment',
                      'pk_intended_reviewer',
                      'filename'
              ]
              #--------------------------------------------------------
              # retrieve data
              #--------------------------------------------------------
              def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, conn=None):
                      if filename is None:
                              filename = self.get_useful_filename(make_unique = True, directory = directory)
                      dl_fname = self.__download_to_file(filename = filename)
                      if dl_fname is None:
                              return None

                      if target_mime is None:
                              return gmMimeLib.adjust_extension_by_mimetype(dl_fname)

                      converted_fname = self.__convert_file_to (
                              filename = dl_fname,
                              target_mime = target_mime,
                              target_extension = target_extension
                      )
                      if converted_fname is None:
                              if ignore_conversion_problems:
                                      return dl_fname
                              return None

                      gmTools.remove_file(dl_fname)
                      return converted_fname

              #--------------------------------------------------------
              def get_reviews(self):
                      SQL = """
                              SELECT
                                      reviewer,
                                      reviewed_when,
                                      is_technically_abnormal,
                                      clinically_relevant,
                                      is_review_by_responsible_reviewer,
                                      is_your_review,
                                      coalesce(comment, '')
                              FROM blobs.v_reviewed_doc_objects
                              WHERE pk_doc_obj = %(pk_doc_obj)s
                              ORDER BY
                                      is_your_review desc,
                                      is_review_by_responsible_reviewer desc,
                                      reviewed_when desc
                              """
                      args = {'pk_doc_obj': self.pk_obj}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      return rows

              #--------------------------------------------------------
              def __get_containing_document(self):
                      return cDocument(aPK_obj = self._payload['pk_doc'])

              containing_document = property(__get_containing_document)

              #--------------------------------------------------------
              def __get_encounter(self):
                      return gmEncounter.cEncounter(aPK_obj = self._payload['pk_encounter'])

              encounter = property(__get_encounter)

              #--------------------------------------------------------
              # store data
              #--------------------------------------------------------
              def update_data_from_incoming(self, conn=None, pk_incoming:int=None):
                      SQL = """
                              UPDATE blobs.doc_obj
                              SET data = (SELECT data FROM clin.incoming_data WHERE pk = %(pk_incoming)s)
                              WHERE pk = %(pk_part)s
                      """
                      args = {'pk_part': self.pk_obj, 'pk_incoming': pk_incoming}
                      gmPG2.run_rw_queries(link_obj = conn, queries = [{'sql': SQL, 'args': args}], return_data = False)
                      # must update XMIN now ...
                      self.refetch_payload(link_obj = conn)
                      return True

              #--------------------------------------------------------
              def update_data_from_file(self, fname=None, link_obj=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

                      cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
                      args = {'pk': self.pk_obj}
                      md5 = gmTools.file2md5(filename = fname, return_hex = True)
                      if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
                              return False

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

              #--------------------------------------------------------
              def set_reviewed(self, technically_abnormal:bool=None, clinically_relevant:bool=None):
                      # row already there ?
                      SQL = """
                              SELECT pk
                              FROM blobs.reviewed_doc_objs
                              WHERE
                                      fk_reviewed_row = %(pk_obj)s and
                                      fk_reviewer = (SELECT pk FROM dem.staff WHERE db_user = current_user)
                      """
                      args = {'pk_obj': self.pk_obj}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                      # INSERT needed
                      if not rows:
                              cols = [
                                      "fk_reviewer",
                                      "fk_reviewed_row",
                                      "is_technically_abnormal",
                                      "clinically_relevant"
                              ]
                              vals = [
                                      '%(fk_row)s',
                                      '%(abnormal)s',
                                      '%(relevant)s'
                              ]
                              args = {
                                      'fk_row': self.pk_obj,
                                      'abnormal': technically_abnormal,
                                      'relevant': clinically_relevant
                              }
                              cmd = """
                                      insert into blobs.reviewed_doc_objs (
                                              %s
                                      ) values (
                                              (SELECT pk FROM dem.staff WHERE db_user=current_user),
                                              %s
                                      )""" % (', '.join(cols), ', '.join(vals))
                      # UPDATE needed
                      elif len(rows) == 1:
                              pk_review = rows[0][0]
                              args = {
                                      'abnormal': technically_abnormal,
                                      'relevant': clinically_relevant,
                                      'pk_review': pk_review
                              }
                              cmd = """
                                      UPDATE blobs.reviewed_doc_objs SET
                                              is_technically_abnormal = %(abnormal)s,
                                              clinically_relevant = %(relevant)s
                                      WHERE
                                              pk = %(pk_review)s
                              """
                      else:
                              raise AssertionError('more than one review by one reviewer for one particular row')

                      rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                      return True

              #--------------------------------------------------------
              def set_as_active_photograph(self):
                      if self._payload['type'] != 'patient photograph':
                              return False

                      # set seq_idx to current max + 1
                      cmd = 'SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s'
                      rows = gmPG2.run_ro_queries (
                              queries = [{
                                      'sql': cmd,
                                      'args': {'doc_id': self._payload['pk_doc']}
                              }]
                      )
                      self._payload['seq_idx'] = rows[0][0]
                      self._is_modified = True
                      return self.save_payload()

              #--------------------------------------------------------
              def reattach(self, pk_doc=None):
                      if pk_doc == self._payload['pk_doc']:
                              return True

                      cmd = """
                              UPDATE blobs.doc_obj SET
                                      fk_doc = %(pk_doc_target)s,
                                      -- coalesce needed for no-parts target docs
                                      seq_idx = (SELECT coalesce(max(seq_idx) + 1, 1) FROM blobs.doc_obj WHERE fk_doc = %(pk_doc_target)s)
                              WHERE
                                      EXISTS(SELECT 1 FROM blobs.doc_med WHERE pk = %(pk_doc_target)s)
                                              AND
                                      pk = %(pk_obj)s
                                              AND
                                      xmin = %(xmin_doc_obj)s
                              RETURNING fk_doc
                      """
                      args = {
                              'pk_doc_target': pk_doc,
                              'pk_obj': self.pk_obj,
                              'xmin_doc_obj': self._payload['xmin_doc_obj']
                      }
                      rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True)
                      if len(rows) == 0:
                              return False
                      # The following should never hold true because the target
                      # fk_doc is returned from the query and it is checked for
                      # equality before the UPDATE already. Assuming the update
                      # failed to update a row because the target fk_doc did
                      # not exist we would not get *any* rows in return - for
                      # which condition we also already checked
                      if rows[0]['fk_doc'] == self._payload['pk_doc']:
                              return False

                      self.refetch_payload()
                      return True

              #--------------------------------------------------------
              def display_via_mime(self, chunksize=0, block=None):

                      fname = self.save_to_file(aChunkSize = chunksize)
                      if fname is None:
                              return False, ''

                      success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
                      if not success:
                              return False, msg

                      return True, ''

              #--------------------------------------------------------
              def format_single_line(self):
                      f_ext = ''
                      if self._payload['filename'] is not None:
                              f_ext = os.path.splitext(self._payload['filename'])[1].strip('.').strip()
                      if f_ext != '':
                              f_ext = ' .' + f_ext.upper()
                      txt = _('part %s, %s%s%s of document %s from %s%s') % (
                              self._payload['seq_idx'],
                              gmTools.size2str(self._payload['size']),
                              f_ext,
                              gmTools.coalesce(self._payload['obj_comment'], '', ' ("%s")'),
                              self._payload['l10n_type'],
                              self._payload['date_generated'].strftime('%Y %b %d'),
                              gmTools.coalesce(self._payload['doc_comment'], '', ' ("%s")')
                      )
                      return txt

              #--------------------------------------------------------
              def format(self, single_line=False):
                      if single_line:
                              return self.format_single_line()

                      txt = _('%s document part                 [#%s]\n') % (
                              gmTools.bool2str (
                                      boolean = self._payload['reviewed'],
                                      true_str = _('Reviewed'),
                                      false_str = _('Unreviewed')
                              ),
                              self._payload['pk_obj']
                      )
                      f_ext = ''
                      if self._payload['filename'] is not None:
                              f_ext = os.path.splitext(self._payload['filename'])[1].strip('.').strip()
                      if f_ext != '':
                              f_ext = '.' + f_ext.upper() + ' '
                      txt += _(' Part %s: %s %s(%s Bytes)\n') % (
                              self._payload['seq_idx'],
                              gmTools.size2str(self._payload['size']),
                              f_ext,
                              self._payload['size']
                      )
                      if self._payload['filename'] is not None:
                              path, fname = os.path.split(self._payload['filename'])
                              if not path.endswith(os.path.sep):
                                      if path != '':
                                              path += os.path.sep
                              if path != '':
                                      path = ' (%s)' % path
                              txt += _(' Filename: %s%s\n') % (fname, path)
                      if self._payload['obj_comment'] is not None:
                              txt += '\n%s\n' % self._payload['obj_comment']
                      return txt

              #--------------------------------------------------------
              def format_metainfo(self, callback=None):
                      """If <callback> is not None it will receive a tuple (status, description, pk_obj)."""
                      if callback is None:
                              return self.__run_metainfo_formatter()

                      gmWorkerThread.execute_in_worker_thread (
                              payload_function = self.__run_metainfo_formatter,
                              completion_callback = callback,
                              worker_name = 'doc_part-metainfo_formatter-'
                      )

              #--------------------------------------------------------
              def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                      patient_part = ''
                      if patient:
                              if name_first:
                                      patient_part = '%s-' % patient.subdir_name
                              else:
                                      patient_part = '-%s' % patient.subdir_name

                      # preserve original filename extension if available
                      suffix = ''
                      if self._payload['filename'] is not None:
                              tmp, suffix = os.path.splitext (
                                      gmTools.fname_sanitize(self._payload['filename']).casefold()
                              )
                      if not suffix:
                              suffix = '.dat'

                      fname_template = '%%s-part_%s' % self._payload['seq_idx']
                      if include_gnumed_tag:
                              fname_template += '-gm_doc'

                      if date_before_type:
                              date_type_part = '%s-%s' % (
                                      self._payload['date_generated'].strftime('%Y-%m-%d'),
                                      self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                              )
                      else:
                              date_type_part = '%s-%s' % (
                                      self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                                      self._payload['date_generated'].strftime('%Y-%m-%d')
                              )

                      if name_first:
                              date_type_name_part = patient_part + date_type_part
                      else:
                              date_type_name_part = date_type_part + patient_part

                      fname = fname_template % date_type_name_part

                      if make_unique:
                              fname = gmTools.get_unique_filename (
                                      prefix = '%s-' % gmTools.fname_sanitize(fname),
                                      suffix = suffix,
                                      tmp_dir = directory
                              )
                      else:
                              fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))
                      return fname

              useful_filename = property(get_useful_filename)

              #--------------------------------------------------------
              # internal helpers
              #--------------------------------------------------------
              def __download_to_file(self, filename=None, aChunkSize=0, conn=None):
                      if self._payload['size'] == 0:
                              _log.debug('part size 0, nothing to download')
                              return None

                      if filename is None:
                              filename = gmTools.get_unique_filename()
                      success = gmPG2.bytea2file (
                              data_query = {
                                      'sql': 'SELECT substring(data FROM %(start)s for %(size)s) FROM blobs.doc_obj WHERE pk=%(pk)s',
                                      'args': {'pk': self.pk_obj}
                              },
                              filename = filename,
                              chunk_size = aChunkSize,
                              data_size = self._payload['size'],
                              conn = conn
                      )
                      if not success:
                              return None

                      return filename

              #--------------------------------------------------------
              def __convert_file_to(self, filename=None, target_mime=None, target_extension=None):
                      assert (filename is not None), '<filename> must not be None'
                      assert (target_mime is not None), '<target_mime> must not be None'

                      if target_extension is None:
                              target_extension = gmMimeLib.guess_ext_by_mimetype(mimetype = target_mime)
                      src_path, src_name = os.path.split(filename)
                      src_stem, src_ext = os.path.splitext(src_name)
                      conversion_tmp_name = gmTools.get_unique_filename (
                              prefix = '%s.conv2.' % src_stem,
                              suffix = target_extension
                      )
                      _log.debug('attempting conversion: [%s] -> [<%s>:%s]', filename, target_mime, conversion_tmp_name)
                      converted_fname = gmMimeLib.convert_file (
                              filename = filename,
                              target_mime = target_mime,
                              target_filename = conversion_tmp_name
                      )
                      if converted_fname is None:
                              _log.warning('conversion failed')
                              return None

                      tmp_path, conv_name = os.path.split(converted_fname)
                      conv_name_in_src_path = os.path.join(src_path, conv_name)
                      try:
                              os.replace(converted_fname, conv_name_in_src_path)
                      except OSError:
                              _log.exception('cannot os.replace(%s, %s)', converted_fname, conv_name_in_src_path)
                              return None

                      return gmMimeLib.adjust_extension_by_mimetype(conv_name_in_src_path)

              #--------------------------------------------------------
              def __run_metainfo_formatter(self):
                      filename = self.__download_to_file()
                      if filename is None:
                              _log.error('problem downloading part')
                              return (False, _('problem downloading document part'))

                      status, desc, cookie = gmMimeLib.describe_file(filename)
                      return (status, desc, self.pk_obj)

  Represents one part of a medical document.

  Call init from child classes like so:

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

  ## Args

  `aPK_obj`
    retrieve data from backend
  - an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
  - a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
  `row`
    must hold the fields
  - data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
  - pk_field: the name of the primary key column OR
  - pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
  - for example:

        row = {
                'data': rows[0],
                'pk_field': 'pk_XXX (the PK column name)',
                'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
        }

        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
        objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `prop containing_document`
    Expand source code

        def __get_containing_document(self):
                return cDocument(aPK_obj = self._payload['pk_doc'])

  `prop encounter`
    Expand source code

        def __get_encounter(self):
                return gmEncounter.cEncounter(aPK_obj = self._payload['pk_encounter'])

  `prop useful_filename`
    Expand source code

        def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                patient_part = ''
                if patient:
                        if name_first:
                                patient_part = '%s-' % patient.subdir_name
                        else:
                                patient_part = '-%s' % patient.subdir_name

                # preserve original filename extension if available
                suffix = ''
                if self._payload['filename'] is not None:
                        tmp, suffix = os.path.splitext (
                                gmTools.fname_sanitize(self._payload['filename']).casefold()
                        )
                if not suffix:
                        suffix = '.dat'

                fname_template = '%%s-part_%s' % self._payload['seq_idx']
                if include_gnumed_tag:
                        fname_template += '-gm_doc'

                if date_before_type:
                        date_type_part = '%s-%s' % (
                                self._payload['date_generated'].strftime('%Y-%m-%d'),
                                self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                        )
                else:
                        date_type_part = '%s-%s' % (
                                self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                                self._payload['date_generated'].strftime('%Y-%m-%d')
                        )

                if name_first:
                        date_type_name_part = patient_part + date_type_part
                else:
                        date_type_name_part = date_type_part + patient_part

                fname = fname_template % date_type_name_part

                if make_unique:
                        fname = gmTools.get_unique_filename (
                                prefix = '%s-' % gmTools.fname_sanitize(fname),
                                suffix = suffix,
                                tmp_dir = directory
                        )
                else:
                        fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))
                return fname

  ### Methods

  `def display_via_mime(self, chunksize=0, block=None)`
    Expand source code

        def display_via_mime(self, chunksize=0, block=None):

                fname = self.save_to_file(aChunkSize = chunksize)
                if fname is None:
                        return False, ''

                success, msg = gmMimeLib.call_viewer_on_file(fname, block = block)
                if not success:
                        return False, msg

                return True, ''

  `def format_metainfo(self, callback=None)`
    Expand source code

        def format_metainfo(self, callback=None):
                """If <callback> is not None it will receive a tuple (status, description, pk_obj)."""
                if callback is None:
                        return self.__run_metainfo_formatter()

                gmWorkerThread.execute_in_worker_thread (
                        payload_function = self.__run_metainfo_formatter,
                        completion_callback = callback,
                        worker_name = 'doc_part-metainfo_formatter-'
                )

    If is not None it will receive a tuple (status, description, pk_obj).

  `def format_single_line(self)`
    Expand source code

        def format_single_line(self):
                f_ext = ''
                if self._payload['filename'] is not None:
                        f_ext = os.path.splitext(self._payload['filename'])[1].strip('.').strip()
                if f_ext != '':
                        f_ext = ' .' + f_ext.upper()
                txt = _('part %s, %s%s%s of document %s from %s%s') % (
                        self._payload['seq_idx'],
                        gmTools.size2str(self._payload['size']),
                        f_ext,
                        gmTools.coalesce(self._payload['obj_comment'], '', ' ("%s")'),
                        self._payload['l10n_type'],
                        self._payload['date_generated'].strftime('%Y %b %d'),
                        gmTools.coalesce(self._payload['doc_comment'], '', ' ("%s")')
                )
                return txt

  `def get_reviews(self)`
    Expand source code

        def get_reviews(self):
                SQL = """
                        SELECT
                                reviewer,
                                reviewed_when,
                                is_technically_abnormal,
                                clinically_relevant,
                                is_review_by_responsible_reviewer,
                                is_your_review,
                                coalesce(comment, '')
                        FROM blobs.v_reviewed_doc_objects
                        WHERE pk_doc_obj = %(pk_doc_obj)s
                        ORDER BY
                                is_your_review desc,
                                is_review_by_responsible_reviewer desc,
                                reviewed_when desc
                        """
                args = {'pk_doc_obj': self.pk_obj}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                return rows

  `def get_useful_filename(self,
  patient=None,
  make_unique=False,
  directory=None,
  include_gnumed_tag=True,
  date_before_type=False,
  name_first=True)`
    Expand source code

        def get_useful_filename(self, patient=None, make_unique=False, directory=None, include_gnumed_tag=True, date_before_type=False, name_first=True):
                patient_part = ''
                if patient:
                        if name_first:
                                patient_part = '%s-' % patient.subdir_name
                        else:
                                patient_part = '-%s' % patient.subdir_name

                # preserve original filename extension if available
                suffix = ''
                if self._payload['filename'] is not None:
                        tmp, suffix = os.path.splitext (
                                gmTools.fname_sanitize(self._payload['filename']).casefold()
                        )
                if not suffix:
                        suffix = '.dat'

                fname_template = '%%s-part_%s' % self._payload['seq_idx']
                if include_gnumed_tag:
                        fname_template += '-gm_doc'

                if date_before_type:
                        date_type_part = '%s-%s' % (
                                self._payload['date_generated'].strftime('%Y-%m-%d'),
                                self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                        )
                else:
                        date_type_part = '%s-%s' % (
                                self._payload['l10n_type'].replace(' ', '_').replace('-', '_'),
                                self._payload['date_generated'].strftime('%Y-%m-%d')
                        )

                if name_first:
                        date_type_name_part = patient_part + date_type_part
                else:
                        date_type_name_part = date_type_part + patient_part

                fname = fname_template % date_type_name_part

                if make_unique:
                        fname = gmTools.get_unique_filename (
                                prefix = '%s-' % gmTools.fname_sanitize(fname),
                                suffix = suffix,
                                tmp_dir = directory
                        )
                else:
                        fname = gmTools.fname_sanitize(os.path.join(gmTools.coalesce(directory, gmTools.gmPaths().tmp_dir), fname + suffix))
                return fname

  `def reattach(self, pk_doc=None)`
    Expand source code

        def reattach(self, pk_doc=None):
                if pk_doc == self._payload['pk_doc']:
                        return True

                cmd = """
                        UPDATE blobs.doc_obj SET
                                fk_doc = %(pk_doc_target)s,
                                -- coalesce needed for no-parts target docs
                                seq_idx = (SELECT coalesce(max(seq_idx) + 1, 1) FROM blobs.doc_obj WHERE fk_doc = %(pk_doc_target)s)
                        WHERE
                                EXISTS(SELECT 1 FROM blobs.doc_med WHERE pk = %(pk_doc_target)s)
                                        AND
                                pk = %(pk_obj)s
                                        AND
                                xmin = %(xmin_doc_obj)s
                        RETURNING fk_doc
                """
                args = {
                        'pk_doc_target': pk_doc,
                        'pk_obj': self.pk_obj,
                        'xmin_doc_obj': self._payload['xmin_doc_obj']
                }
                rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True)
                if len(rows) == 0:
                        return False
                # The following should never hold true because the target
                # fk_doc is returned from the query and it is checked for
                # equality before the UPDATE already. Assuming the update
                # failed to update a row because the target fk_doc did
                # not exist we would not get *any* rows in return - for
                # which condition we also already checked
                if rows[0]['fk_doc'] == self._payload['pk_doc']:
                        return False

                self.refetch_payload()
                return True

  `def save_to_file(self,
  aChunkSize=0,
  filename=None,
  target_mime=None,
  target_extension=None,
  ignore_conversion_problems=False,
  directory=None,
  conn=None)`
    Expand source code

        def save_to_file(self, aChunkSize=0, filename=None, target_mime=None, target_extension=None, ignore_conversion_problems=False, directory=None, conn=None):
                if filename is None:
                        filename = self.get_useful_filename(make_unique = True, directory = directory)
                dl_fname = self.__download_to_file(filename = filename)
                if dl_fname is None:
                        return None

                if target_mime is None:
                        return gmMimeLib.adjust_extension_by_mimetype(dl_fname)

                converted_fname = self.__convert_file_to (
                        filename = dl_fname,
                        target_mime = target_mime,
                        target_extension = target_extension
                )
                if converted_fname is None:
                        if ignore_conversion_problems:
                                return dl_fname
                        return None

                gmTools.remove_file(dl_fname)
                return converted_fname

  `def set_as_active_photograph(self)`
    Expand source code

        def set_as_active_photograph(self):
                if self._payload['type'] != 'patient photograph':
                        return False

                # set seq_idx to current max + 1
                cmd = 'SELECT coalesce(max(seq_idx)+1, 1) FROM blobs.doc_obj WHERE fk_doc = %(doc_id)s'
                rows = gmPG2.run_ro_queries (
                        queries = [{
                                'sql': cmd,
                                'args': {'doc_id': self._payload['pk_doc']}
                        }]
                )
                self._payload['seq_idx'] = rows[0][0]
                self._is_modified = True
                return self.save_payload()

  `def set_reviewed(self, technically_abnormal: bool = None, clinically_relevant: bool = None)`
    Expand source code

        def set_reviewed(self, technically_abnormal:bool=None, clinically_relevant:bool=None):
                # row already there ?
                SQL = """
                        SELECT pk
                        FROM blobs.reviewed_doc_objs
                        WHERE
                                fk_reviewed_row = %(pk_obj)s and
                                fk_reviewer = (SELECT pk FROM dem.staff WHERE db_user = current_user)
                """
                args = {'pk_obj': self.pk_obj}
                rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                # INSERT needed
                if not rows:
                        cols = [
                                "fk_reviewer",
                                "fk_reviewed_row",
                                "is_technically_abnormal",
                                "clinically_relevant"
                        ]
                        vals = [
                                '%(fk_row)s',
                                '%(abnormal)s',
                                '%(relevant)s'
                        ]
                        args = {
                                'fk_row': self.pk_obj,
                                'abnormal': technically_abnormal,
                                'relevant': clinically_relevant
                        }
                        cmd = """
                                insert into blobs.reviewed_doc_objs (
                                        %s
                                ) values (
                                        (SELECT pk FROM dem.staff WHERE db_user=current_user),
                                        %s
                                )""" % (', '.join(cols), ', '.join(vals))
                # UPDATE needed
                elif len(rows) == 1:
                        pk_review = rows[0][0]
                        args = {
                                'abnormal': technically_abnormal,
                                'relevant': clinically_relevant,
                                'pk_review': pk_review
                        }
                        cmd = """
                                UPDATE blobs.reviewed_doc_objs SET
                                        is_technically_abnormal = %(abnormal)s,
                                        clinically_relevant = %(relevant)s
                                WHERE
                                        pk = %(pk_review)s
                        """
                else:
                        raise AssertionError('more than one review by one reviewer for one particular row')

                rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                return True

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

        def update_data_from_file(self, fname=None, link_obj=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

                cmd = "UPDATE blobs.doc_obj SET data = %(data)s::BYTEA WHERE pk = %(pk)s RETURNING md5(data) AS md5"
                args = {'pk': self.pk_obj}
                md5 = gmTools.file2md5(filename = fname, return_hex = True)
                if not gmPG2.file2bytea(conn = link_obj, query = cmd, filename = fname, args = args, file_md5 = md5):
                        return False

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

  `def update_data_from_incoming(self, conn=None, pk_incoming: int = None)`
    Expand source code

        def update_data_from_incoming(self, conn=None, pk_incoming:int=None):
                SQL = """
                        UPDATE blobs.doc_obj
                        SET data = (SELECT data FROM clin.incoming_data WHERE pk = %(pk_incoming)s)
                        WHERE pk = %(pk_part)s
                """
                args = {'pk_part': self.pk_obj, 'pk_incoming': pk_incoming}
                gmPG2.run_rw_queries(link_obj = conn, queries = [{'sql': SQL, 'args': args}], return_data = False)
                # must update XMIN now ...
                self.refetch_payload(link_obj = conn)
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cDocumentType (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      class cDocumentType(gmBusinessDBObject.cBusinessDBObject):
              """Represents a document type."""
              _cmd_fetch_payload = """SELECT * FROM blobs.v_doc_type WHERE pk_doc_type=%s"""
              _cmds_store_payload = [
                      """update blobs.doc_type set
                                      name = %(type)s
                              WHERE
                                      pk=%(pk_obj)s and
                                      xmin=%(xmin_doc_type)s""",
                      """SELECT xmin_doc_type FROM blobs.v_doc_type WHERE pk_doc_type = %(pk_obj)s"""
              ]
              _updatable_fields = ['type']
              #--------------------------------------------------------
              def set_translation(self, translation=None):
                      if translation.strip() == '':
                              return False

                      if translation.strip() == self._payload['l10n_type'].strip():
                              return True

                      args = {
                              'orig': self._payload['type'],
                              'tx': translation
                      }
                      queries = [{
                              'sql': 'SELECT i18n.i18n(%(orig)s)',
                              'args': args
                      }, {
                              'sql': 'SELECT i18n.upd_tx((SELECT i18n.get_curr_lang()), %(orig)s, %(tx)s)',
                              'args': args
                      }]
                      rows = gmPG2.run_rw_queries(queries = queries, return_data = True)
                      if not rows[0][0]:
                              _log.error('cannot set translation to [%s]' % translation)
                              return False

                      return self.refetch_payload()

  Represents a document type.

  Call init from child classes like so:

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

  ## Args

  `aPK_obj`
    retrieve data from backend
  - an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
  - a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
  `row`
    must hold the fields
  - data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
  - pk_field: the name of the primary key column OR
  - pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
  - for example:

        row = {
                'data': rows[0],
                'pk_field': 'pk_XXX (the PK column name)',
                'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
        }

        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
        objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]

  ### Ancestors

  - cBusinessDBObject

  ### Methods

  `def set_translation(self, translation=None)`
    Expand source code

        def set_translation(self, translation=None):
                if translation.strip() == '':
                        return False

                if translation.strip() == self._payload['l10n_type'].strip():
                        return True

                args = {
                        'orig': self._payload['type'],
                        'tx': translation
                }
                queries = [{
                        'sql': 'SELECT i18n.i18n(%(orig)s)',
                        'args': args
                }, {
                        'sql': 'SELECT i18n.upd_tx((SELECT i18n.get_curr_lang()), %(orig)s, %(tx)s)',
                        'args': args
                }]
                rows = gmPG2.run_rw_queries(queries = queries, return_data = True)
                if not rows[0][0]:
                        _log.error('cannot set translation to [%s]' % translation)
                        return False

                return self.refetch_payload()

  ### Inherited members

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