Query Builder

A wrapper around the PyBEL query builder.

exception pybel_tools.query.QueryMissingNetworksError

Raised if a query is created from json but doesn’t have a listing of network identifiers.

class pybel_tools.query.Query(network_ids=None, seeding=None, pipeline=None)

Represents a query over a network store.

Build a query.

Parameters:network_ids (None or int or iter[int]) – Database network identifiers identifiers

append_network(network_id)

Add a network to this query.

Parameters:network_id (int) – The database identifier of the network Returns:self for fluid API Return type:Query

append_seeding_induction(nodes)

Add a seed induction method.

Parameters:or Node or BaseEntity] nodes (list[tuple) – A list of PyBEL node tuples Returns:seeding container for fluid API Return type:Seeding

append_seeding_neighbors(nodes)

Add a seed by neighbors.

Parameters:nodes (BaseEntity or iter[BaseEntity]) – A list of PyBEL node tuples

append_seeding_annotation(annotation, values)

Add a seed induction method for single annotation’s values.

Parameters:

• annotation (str) – The annotation to filter by
• values (set[str]) – The values of the annotation to keep

append_seeding_sample(**kwargs)

Add seed induction methods.

Kwargs can have number_edges or number_seed_nodes.

append_pipeline(name, *args, **kwargs)

Add an entry to the pipeline. Defers to pybel_tools.pipeline.Pipeline.append().

Parameters:name (str or types.FunctionType) – The name of the function Returns:This pipeline for fluid query building Return type:Pipeline

run(manager)

Run this query and returns the resulting BEL graph.

Parameters:manager – A cache manager Return type:Optional[pybel.BELGraph]

to_json()

Return this query as a JSON object.

Return type:dict

dump(file, **kwargs)

Dump this query to a file as JSON.

dumps(**kwargs)

Dump this query to a string as JSON

Return type:str

static from_json(data)

Load a query from a JSON dictionary.

Parameters:data (dict) – A JSON dictionary Return type:Query Raises:QueryMissingNetworksError

static load(file)

Load a query from a JSON file.

Parameters:file – A file or file-like Return type:Query Raises:QueryMissingNetworksError

static loads(s)

Load a query from a JSON string

Parameters:s (str) – A stringified JSON query Return type:Query Raises:QueryMissingNetworksError