cobra.io.web
============

.. py:module:: cobra.io.web

.. autoapi-nested-parse::

   Provide functionality to access remote model repositories.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/cobra/io/web/abstract_model_repository/index
   /autoapi/cobra/io/web/bigg_models_repository/index
   /autoapi/cobra/io/web/biomodels_repository/index
   /autoapi/cobra/io/web/cobrapy_repository/index
   /autoapi/cobra/io/web/load/index


Classes
-------

.. autoapisummary::

   cobra.io.web.AbstractModelRepository
   cobra.io.web.BiGGModels
   cobra.io.web.BioModels


Functions
---------

.. autoapisummary::

   cobra.io.web.load_model


Package Contents
----------------

.. py:class:: AbstractModelRepository(*, url: Union[httpx.URL, str], **kwargs)

   Bases: :py:obj:`abc.ABC`


   Define an abstract base class that describes a remote model repository.

   .. attribute:: name

      The name of the remote repository.

      :type: str


   .. py:attribute:: _progress


   .. py:attribute:: name
      :type:  str
      :value: 'Abstract'



   .. py:attribute:: _url


   .. py:property:: url
      :type: httpx.URL


      Return the repository's URL.


   .. py:method:: get_sbml(model_id: str) -> bytes
      :abstractmethod:


      Attempt to download an SBML document from the repository.

      :param model_id: The identifier of the desired metabolic model. This is typically repository
                       specific.
      :type model_id: str

      :returns: A gzip-compressed, UTF-8 encoded SBML document.
      :rtype: bytes



.. py:class:: BiGGModels(**kwargs)

   Bases: :py:obj:`cobra.io.web.abstract_model_repository.AbstractModelRepository`


   Define a concrete implementation of the BiGG Models repository.

   .. attribute:: name

      The name of the BiGG Models repository.

      :type: str


   .. py:attribute:: name
      :type:  str
      :value: 'BiGG Models'



   .. py:method:: get_sbml(model_id: str) -> bytes

      Attempt to download an SBML document from the repository.

      :param model_id: The identifier of the desired metabolic model. This is typically repository
                       specific.
      :type model_id: str

      :returns: A gzip-compressed, UTF-8 encoded SBML document.
      :rtype: bytes

      :raises httpx.HTTPError: In case there are any connection problems.



.. py:class:: BioModels(**kwargs)

   Bases: :py:obj:`cobra.io.web.abstract_model_repository.AbstractModelRepository`


   Define a concrete implementation of the BioModels repository.

   .. attribute:: name

      The name of the BioModels repository.

      :type: str


   .. py:attribute:: name
      :type:  str
      :value: 'BioModels'



   .. py:method:: get_sbml(model_id: str) -> bytes

      Attempt to download an SBML document from the repository.

      :param model_id: The identifier of the desired metabolic model. This is typically repository
                       specific.
      :type model_id: str

      :returns: A gzip-compressed, UTF-8 encoded SBML document.
      :rtype: bytes

      :raises httpx.HTTPError: In case there are any connection problems.



.. py:function:: load_model(model_id: str, repositories: Iterable[cobra.io.web.abstract_model_repository.AbstractModelRepository] = DEFAULT_REPOSITORIES, cache: bool = True) -> cobra.core.Model

   Download an SBML model from a remote repository.

   Downloaded SBML documents are by default stored in a cache on disk such that future
   access is much faster. By default, models can be loaded from the following
   repositories:

   * BiGG Models
   * BioModels

   You can use the ``AbstractModelRepository`` class as a parent to implement your own
   repository accessor which you pass to the ``load_model`` function. In case you
   implement a new interface, please consider submitting a pull request to COBRApy.

   :param model_id: The identifier of the desired metabolic model. This is typically repository
                    specific.
   :type model_id: str
   :param repositories: An iterable of repository accessor instances. The model_id is searched in order.
   :type repositories: iterable, optional

   :returns: A model instance generated from the SBML document.
   :rtype: Model

   :raises RuntimeError: As with any internet connection, there are multiple errors that can occur.

   .. rubric:: Examples

   # Most of the time calling `load_model` with an identifier should be enough.
   >>> print(load_model("e_coli_core"))
   e_coli_core
   >>> print(load_model("MODEL1510010000"))
   MODEL1510010000

   .. seealso:: :py:obj:`BiGGModels`, :py:obj:`BioModels`