biggr_models.queries.model_queries

biggr_models.queries.model_queries#

Classes#

TreeNode

TaxonTreeNode

CollectionTreeNode

ModelTreeNode

Functions#

get_models_count(session, **kwargs)

Return the number of models in the database.

get_models(session[, page, size, sort_column, ...])

Get models and number of components.

get_model_and_counts(model_bigg_id, session[, ...])

get_model_list(session)

Return a list of all models, for advanced search.

get_model_json_string(model_bigg_id)

Get the model JSON for download.

get_model_object(session, id)

get_taxons_recursively(session, starting_id)

get_model_collections_and_taxons(session)

Module Contents#

biggr_models.queries.model_queries.get_models_count(session, **kwargs)#

Return the number of models in the database.

biggr_models.queries.model_queries.get_models(session, page=None, size=None, sort_column=None, sort_direction='ascending')#

Get models and number of components.

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',)

  • 'organism'

  • 'metabolite_count'

  • 'reaction_count'

  • 'gene_count'. (and)

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

Returns:

  • A list of objects with keys ‘bigg_id’, ‘organism’, ‘metabolite_count’,

  • ’reaction_count’, and ‘gene_count’.

biggr_models.queries.model_queries.get_model_and_counts(model_bigg_id, session, static_model_dir=None)#
biggr_models.queries.model_queries.get_model_list(session)#

Return a list of all models, for advanced search.

biggr_models.queries.model_queries.get_model_json_string(model_bigg_id)#

Get the model JSON for download.

biggr_models.queries.model_queries.get_model_object(session: sqlalchemy.orm.Session, id: biggr_models.queries.utils.IDType)#
biggr_models.queries.model_queries.get_taxons_recursively(session: sqlalchemy.orm.Session, starting_id: int | Iterable[int])#
class biggr_models.queries.model_queries.TreeNode#
name: str#
children: List[TreeNode]#
recursive_collapse(parent=None, stops=None)#
property node_type#
class biggr_models.queries.model_queries.TaxonTreeNode#

Bases: TreeNode

tax_id: int#
rank_id: int#
hidden_taxons: List[Tuple[int, str, int]] | None = None#
recursive_collapse(parent=None, stops=None)#
class biggr_models.queries.model_queries.CollectionTreeNode#

Bases: TreeNode

collection: cobradb.models.ModelCollection#
recursive_collapse(parent=None, stops=None)#
class biggr_models.queries.model_queries.ModelTreeNode#

Bases: TreeNode

model: cobradb.models.Model#
biggr_models.queries.model_queries.get_model_collections_and_taxons(session: sqlalchemy.orm.Session)#