biggr_models.queries.model_queries
==================================

.. py:module:: biggr_models.queries.model_queries


Classes
-------

.. autoapisummary::

   biggr_models.queries.model_queries.TreeNode
   biggr_models.queries.model_queries.TaxonTreeNode
   biggr_models.queries.model_queries.CollectionTreeNode
   biggr_models.queries.model_queries.ModelTreeNode


Functions
---------

.. autoapisummary::

   biggr_models.queries.model_queries.get_models_count
   biggr_models.queries.model_queries.get_models
   biggr_models.queries.model_queries.get_model_and_counts
   biggr_models.queries.model_queries.get_model_list
   biggr_models.queries.model_queries.get_model_json_string
   biggr_models.queries.model_queries.get_model_object
   biggr_models.queries.model_queries.get_taxons_recursively
   biggr_models.queries.model_queries.get_model_collections_and_taxons


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

.. py:function:: get_models_count(session, **kwargs)

   Return the number of models in the database.


.. py:function:: get_models(session, page=None, size=None, sort_column=None, sort_direction='ascending')

   Get models and number of components.

   :param session:
   :type session: An ome session object.
   :param page:
   :type page: The page, or None for all pages.
   :param size:
   :type size: The page length, or None for all pages.
   :param sort_column:
   :type sort_column: The name of the column to sort. Must be one of 'bigg_id',
   :param 'organism':
   :param 'metabolite_count':
   :param 'reaction_count':
   :param and 'gene_count'.:
   :param sort_direction:
   :type sort_direction: Either 'ascending' or 'descending'.

   :returns: * *A list of objects with keys 'bigg_id', 'organism', 'metabolite_count',*
             * *'reaction_count', and 'gene_count'.*


.. py:function:: get_model_and_counts(model_bigg_id, session, static_model_dir=None)

.. py:function:: get_model_list(session)

   Return a list of all models, for advanced search.


.. py:function:: get_model_json_string(model_bigg_id)

   Get the model JSON for download.


.. py:function:: get_model_object(session: sqlalchemy.orm.Session, id: biggr_models.queries.utils.IDType)

.. py:function:: get_taxons_recursively(session: sqlalchemy.orm.Session, starting_id: Union[int, Iterable[int]])

.. py:class:: TreeNode

   .. py:attribute:: name
      :type:  str


   .. py:attribute:: children
      :type:  List[TreeNode]


   .. py:method:: recursive_collapse(parent=None, stops=None)


   .. py:property:: node_type


.. py:class:: TaxonTreeNode

   Bases: :py:obj:`TreeNode`


   .. py:attribute:: tax_id
      :type:  int


   .. py:attribute:: rank_id
      :type:  int


   .. py:attribute:: hidden_taxons
      :type:  Optional[List[Tuple[int, str, int]]]
      :value: None



   .. py:method:: recursive_collapse(parent=None, stops=None)


.. py:class:: CollectionTreeNode

   Bases: :py:obj:`TreeNode`


   .. py:attribute:: collection
      :type:  cobradb.models.ModelCollection


   .. py:method:: recursive_collapse(parent=None, stops=None)


.. py:class:: ModelTreeNode

   Bases: :py:obj:`TreeNode`


   .. py:attribute:: model
      :type:  cobradb.models.Model


.. py:function:: get_model_collections_and_taxons(session: sqlalchemy.orm.Session)