s1a_get_pathway.py

#!/usr/bin/env python
"""Retrieving a pathway based on its identifier.
# https://reactome.org/dev/graph-database/extract-participating-molecules#retrieving-objects

Usage: s1a_get_pathway.py <neo4j_password> [options]

Options:
  -h --help  Show usage
  -u --neo4j_username=USER  Neo4j Reactome username [default: neo4j]
  --url=URL                 Neo4j Reactome local url [default: bolt://localhost:7687]
"""

from __future__ import print_function
from reactomepy.code.utils import get_gdbdr

__copyright__ = "Copyright (C) 2018-present, DV Klopfenstein. All rights reserved."
__author__ = "DV Klopfenstein"

import sys
from neo4j import GraphDatabase


def main(password):
    """Retrieving a pathway based on its identifier."""
    # To retrieve the Pathway "Antigen processing-Cross presentation" with identifier R-HSA-1236975:
    qry = 'MATCH (pathway:Pathway{stId:"R-HSA-1236975"}) RETURN pathway'

    gdbdr = GraphDatabase.driver('bolt://localhost:7687', auth=('neo4j', password))
    print(qry)
    with gdbdr.session() as session:
        for dct in session.run(qry).data():
            for key, val in dct['pathway'].items():
                print("    {KEY:11} {VAL}".format(KEY=key, VAL=val))


if __name__ == '__main__':
    assert len(sys.argv) != 1, 'First arg must be your Neo4j database password'
    main(sys.argv[1])

# Copyright (C) 2018-present, DV Klopfenstein. All rights reserved.