biggr_models.queries.reaction_queries

biggr_models.queries.reaction_queries#

Attributes#

REF_ANNOTATIONS_SUBQ

REACTION_ANNOTATIONS_SUBQ

Functions#

get_universal_reactions_count(session)

Return the number of universal reactions.

get_universal_reactions(session[, page, size, ...])

Get universal reactions.

get_model_reactions_count(model_bigg_id, session)

Count the model reactions.

get_model_reactions(model_bigg_id, session[, page, ...])

Get model reactions.

get_universal_reaction_and_models(→ Dict[str, Any])

get_reactions_for_model(model_bigg_id, session)

get_model_list_for_reaction(reaction_bigg_id, session)

get_reference_for_reaction(reaction_bigg_id, session)

get_model_reaction(model_bigg_id, biggr_id, session)

Get details about this reaction in the given model. Returns multiple

get_reaction(reaction_bigg_id, session)

get_reaction_object(→ Dict[str, Any])

Module Contents#

biggr_models.queries.reaction_queries.get_universal_reactions_count(session)#

Return the number of universal reactions.

biggr_models.queries.reaction_queries.get_universal_reactions(session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)#

Get universal reactions.

Parameters:

  • session (An ome session object.)

  • page (The page, or None for all pages.)

  • size (The page length, or None for all pages.)

  • sort_column (The name of the column to sort. Must be one of 'bigg_id', 'name'.)

  • sort_direction (Either 'ascending' or 'descending'.)

Return type:

A list of objects with keys ‘bigg_id’, ‘name’.

biggr_models.queries.reaction_queries.get_model_reactions_count(model_bigg_id, session)#

Count the model reactions.

biggr_models.queries.reaction_queries.get_model_reactions(model_bigg_id, session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)#

Get model reactions.

Parameters:

  • model_bigg_id (The bigg id of the model to retrieve reactions.)

  • session (An ome session object.)

  • page (The page, or None for all pages.)

  • size (The page length, or None for all pages.)

  • sort_column (The name of the column to sort. Must be one of 'bigg_id', 'name',)

  • 'model_bigg_id'

  • 'organism'. (and)

  • sort_direction (Either 'ascending' or 'descending'.)

Returns:

  • A list of objects with keys ‘bigg_id’, ‘name’, ‘model_bigg_id’, and

  • ’organism’.

biggr_models.queries.reaction_queries.get_universal_reaction_and_models(session: sqlalchemy.orm.Session, reaction_bigg_id: str) → Dict[str, Any]#
biggr_models.queries.reaction_queries.get_reactions_for_model(model_bigg_id, session)#
biggr_models.queries.reaction_queries.get_model_list_for_reaction(reaction_bigg_id, session)#
biggr_models.queries.reaction_queries.get_reference_for_reaction(reaction_bigg_id, session)#
biggr_models.queries.reaction_queries.get_model_reaction(model_bigg_id, biggr_id, session)#

Get details about this reaction in the given model. Returns multiple results when the reaction appears in the model multiple times.

biggr_models.queries.reaction_queries.get_reaction(reaction_bigg_id, session)#
biggr_models.queries.reaction_queries.REF_ANNOTATIONS_SUBQ#
biggr_models.queries.reaction_queries.REACTION_ANNOTATIONS_SUBQ#
biggr_models.queries.reaction_queries.get_reaction_object(session: sqlalchemy.orm.Session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True) → Dict[str, Any]#