Gnumed.business.gmCoding API documentation
Description: GNUmed coding systems handling middleware

# Module `Gnumed.business.gmCoding`

GNUmed coding systems handling middleware

## Functions

`def create_data_source(long_name=None, short_name=None, version=None, source=None, language=None)`
  Expand source code

      def create_data_source(long_name=None, short_name=None, version=None, source=None, language=None):

                      args = {
                              'lname': long_name,
                              'sname': short_name,
                              'ver': version,
                              'src': source,
                              'lang': language
                      }

                      cmd = "SELECT pk FROM ref.data_source WHERE name_long = %(lname)s AND name_short = %(sname)s AND version = %(ver)s"
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      if len(rows) > 0:
                              return rows[0]['pk']

                      cmd = """
                              INSERT INTO ref.data_source (name_long, name_short, version, source, lang)
                              VALUES (
                                      %(lname)s,
                                      %(sname)s,
                                      %(ver)s,
                                      %(src)s,
                                      %(lang)s
                              )
                              RETURNING pk
                      """
                      rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True)

                      return rows[0]['pk']

`def get_coded_terms(coding_systems=None, languages=None, order_by=None)`
  Expand source code

      def get_coded_terms(coding_systems=None, languages=None, order_by=None):

              where_snippets = []
              args = {}

              if coding_systems is not None:
                      where_snippets.append("((coding_system = ANY(%(sys)s)) OR (coding_system_long = ANY(%(sys)s))")
                      args['sys'] = coding_systems

              if languages is not None:
                      where_snippets.append('lang = ANY(%(lang)s)')
                      args['lang'] = languages

              cmd = 'select * from ref.v_coded_terms'

              if len(where_snippets) > 0:
                      cmd += ' WHERE %s' % ' AND '.join(where_snippets)

              if order_by is not None:
                      cmd += ' ORDER BY %s' % order_by

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

              return rows

`def get_data_sources(order_by='name_long, lang, version')`
  Expand source code

      def get_data_sources(order_by='name_long, lang, version'):
              cmd = 'SELECT * FROM ref.data_source ORDER BY %s' % order_by
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}])
              return rows

`def get_generic_codes(order_by=None)`
  Expand source code

      def get_generic_codes(order_by=None):
              if order_by is None:
                      order_by = 'true'
              else:
                      order_by = 'true ORDER BY %s' % order_by

              cmd = _SQL_get_generic_code % order_by
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}])
              return [ cGenericCode(row = {'data': r, 'pk_field': 'pk_generic_code'}) for r in rows ]

`def get_generic_linked_codes(order_by=None)`
  Expand source code

      def get_generic_linked_codes(order_by=None):
              if order_by is None:
                      order_by = 'true'
              else:
                      order_by = 'true ORDER BY %s' % order_by

              cmd = _SQL_get_generic_linked_codes % order_by
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}])
              return [ cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ]

## Classes

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

      class cGenericCode(gmBusinessDBObject.cBusinessDBObject):
              """READ ONLY"""
              _cmd_fetch_payload = _SQL_get_generic_code % "pk_generic_code = %s"
              _cmds_store_payload:list = []
              _updatable_fields:list = []

  READ ONLY

  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

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

      class cGenericLinkedCode(gmBusinessDBObject.cBusinessDBObject):
              """Represents a generic linked code.

              READ ONLY
              """
              _cmd_fetch_payload = _SQL_get_generic_linked_codes % "pk_lnk_code2item = %s"
              _cmds_store_payload:list = []
              _updatable_fields:list = []

  Represents a generic linked code.

  READ ONLY

  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

  ### 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`