modos.helpers.schema
====================

.. py:module:: modos.helpers.schema

.. autoapi-nested-parse::

   Introspection utilities for the MODO schema.

   This module provides helpers for accessing the schema structure
   and for converting instances to different representations.



Attributes
----------

.. autoapisummary::

   modos.helpers.schema.SCHEMA_PATH


Classes
-------

.. autoapisummary::

   modos.helpers.schema.UserElementType
   modos.helpers.schema.ElementType


Functions
---------

.. autoapisummary::

   modos.helpers.schema.class_from_name
   modos.helpers.schema.dict_to_instance
   modos.helpers.schema.is_full_id
   modos.helpers.schema.set_haspart_relationship
   modos.helpers.schema.update_haspart_id
   modos.helpers.schema.set_data_path
   modos.helpers.schema.is_uri
   modos.helpers.schema.load_schema
   modos.helpers.schema.load_prefixmap
   modos.helpers.schema.get_slots
   modos.helpers.schema.instance_to_graph
   modos.helpers.schema.get_slot_range
   modos.helpers.schema.get_enum_values
   modos.helpers.schema.get_haspart_property


Module Contents
---------------

.. py:data:: SCHEMA_PATH

.. py:function:: class_from_name(name)

.. py:function:: dict_to_instance(element)

.. py:function:: is_full_id(element_id)

   Checks if an element_id contains the element type as prefix.

   .. rubric:: Examples

   >>> is_full_id("sample1")
   False
   >>> is_full_id("data/test")
   True
   >>> is_full_id("/assay/test_assay")
   True


.. py:function:: set_haspart_relationship(child_class, child_path, parent_group)

   Add element to the hasPart attribute of a parent zarr group


.. py:function:: update_haspart_id(element)

   update the id of the has_part property of an element to use the full id including its type


.. py:function:: set_data_path(element, source_file = None)

   Set the data_path attribute, if it is not specified to the modo root.


.. py:class:: UserElementType

   Bases: :py:obj:`str`, :py:obj:`enum.Enum`


   Enumeration of element types exposed to the user.


   .. py:attribute:: SAMPLE
      :value: 'sample'



   .. py:attribute:: ASSAY
      :value: 'assay'



   .. py:attribute:: DATA_ENTITY
      :value: 'data'



   .. py:attribute:: REFERENCE_GENOME
      :value: 'reference'



   .. py:method:: get_target_class()

      Return the target class for the element type.



   .. py:method:: from_object(obj)
      :classmethod:


      Return the element type from an object.



.. py:class:: ElementType

   Bases: :py:obj:`str`, :py:obj:`enum.Enum`


   Enumeration of all element types.


   .. py:attribute:: SAMPLE
      :value: 'sample'



   .. py:attribute:: ASSAY
      :value: 'assay'



   .. py:attribute:: DATA_ENTITY
      :value: 'data'



   .. py:attribute:: REFERENCE_GENOME
      :value: 'reference'



   .. py:attribute:: REFERENCE_SEQUENCE
      :value: 'sequence'



   .. py:method:: get_target_class()

      Return the target class for the element type.



   .. py:method:: from_object(obj)
      :classmethod:


      Return the element type from an object.



   .. py:method:: from_model_name(name)
      :classmethod:


      Return the element type from an object name.



.. py:function:: is_uri(text)

   Checks if input is a valid URI.


.. py:function:: load_schema()

   Return a view over the schema structure.


.. py:function:: load_prefixmap()

   Load the prefixmap.


.. py:function:: get_slots(target_class, required_only=False)

   Return a list of required slots for a class.


.. py:function:: instance_to_graph(instance)

.. py:function:: get_slot_range(slot_name)

   Return the class-independent range of a slot.


.. py:function:: get_enum_values(enum_name)

.. py:function:: get_haspart_property(child_class)

   Return the name of the "has_part" property for a target class.
   If no such property is in the schema, return None.

   .. rubric:: Examples

   >>> get_haspart_property('AlignmentSet')
   'has_data'
   >>> get_haspart_property('Assay')
   'has_assay'