PatternExecutor#

class biopax-explorer.pattern.pattern.PatternExecutor(db=None, dataset=None, blacklist=None, doProcess=True)[source]#

Bases: PatternExecutor

This class manages the execution of a ‘Pattern’ instance.

Args:

gen_utils (module): Meta model python module from the target domain module (biopax). db (str): Database name for API connection. dataset (str): Dataset name for API connection. blacklist (list): A list of entities to be excluded. doProcess (bool): True to activate (default is True).

Methods

createQueryBuilder([add_children])	Creates a query builder.
datasetFile(dataset_file)	Defines the source RDF/XML file to use as an in-memory graph.
difference(part, col)	Computes the difference between two sets of entities.
executeLocalProcessing(lp, inputCollection)	Executes local processing.
executePattern(p[, by_reference, max_count])	Executes a pattern.
executePatternImpl(p, simul)	Executes a pattern.
executeSparqlQuery(query, ml[, do_pk_only, ...])	Executes a SPARQL query.
fetchEntities(p[, level, max_count])	Fetches entities based on a pattern.
intersection(part, col)	Computes the intersection of two sets of entities.
limit(climit)	Sets the limit for internal use.
log(*msg)	Logs messages.
maxCount(mcount)	Sets the maximum count for testing purposes.
operatorProcess(op, resultQ, resultFinal)	Applies set operations (UNION, INTERSECTION, DIFFERENCE) to the result.
pump(resultFin[, level])	Pumps the result.
pumpImpl(inputInstDict[, level])	Implements the pumping process.
queries(p)	Generates queries for a pattern.
steplog(*msg)	Logs messages related to steps.
testType(res, tag)	Tests the type of result.
union(part, col)	Computes the union of two sets of entities.
validate_processed_steps()	Validates processed steps.
verbose([verb])	Sets verbosity for debug mode.