import sys
import rdflib
import json
import urllib2
from processor import BelProcessor
import ndex_client

def process_ndex_neighborhood(gene_names, rdf_out='bel_output.rdf'):
    network_id = '9ea3c170-01ad-11e5-ac0f-000c29cb28fb'
    #url_suffix = '/bel2rdf/v1/network/%s/asBELRDF/query' % network_id
    url_suffix = '/network/%s/asBELRDF/query' % network_id
    params = {'searchString': ' '.join(gene_names)}
    rdf = ndex_client.send_request(url_suffix, params)
    if rdf is None:
        print 'No response for NDEx neighborhood query.'
        return None
    with open(rdf_out, 'wt') as fh:
        fh.write(rdf.encode('utf-8'))
    bp = process_belrdf(rdf)
    return bp


def process_belrdf(rdf_str):
    # Parse the RDF
    g = rdflib.Graph()
    g.parse(data=rdf_str, format='nt')
    # Build INDRA statements from RDF
    bp = BelProcessor(g)
    bp.get_complexes()
    bp.get_activating_subs()
    bp.get_modifications()
    bp.get_dephosphorylations()
    bp.get_activating_mods()
    bp.get_composite_activating_mods()
    bp.get_activity_activity()

    # Print some output about the process
    bp.print_statement_coverage()
    print "\n--- Converted INDRA Statements -------------"
    bp.print_statements()
    return bp

if __name__ == '__main__':
    # Make sure the user passed in an RDF filename
    if len(sys.argv) < 2:
        print "Usage: python bel_api.py file.rdf"
        sys.exit()
    # We take the RDF filename as the argument
    rdf_filename = sys.argv[1]
    bp = process_belrdf(open(rdf_filename).read())

import sys
import rdflib
from rdflib.plugins.parsers.ntriples import ParseError
import json
import urllib2
from processor import BelProcessor
import ndex_client

def process_ndex_neighborhood(gene_names, rdf_out='bel_output.rdf'):
    network_id = '9ea3c170-01ad-11e5-ac0f-000c29cb28fb'
    #url_suffix = '/bel2rdf/v1/network/%s/asBELRDF/query' % network_id
    url_suffix = '/network/%s/asBELRDF/query' % network_id
    params = {'searchString': ' '.join(gene_names)}
    rdf = ndex_client.send_request(url_suffix, params)
    if rdf is None:
        print 'No response for NDEx neighborhood query.'
        return None
    with open(rdf_out, 'wt') as fh:
        fh.write(rdf.encode('utf-8'))
    bp = process_belrdf(rdf)
    return bp


def process_belrdf(rdf_str):
    """Process a BEL RDF string and process and return a
    BEL processor.
    """
    g = rdflib.Graph()
    try:
        g.parse(data=rdf_str, format='nt')
    except ParseError:
        print 'Could not parse rdf.'
        return None
    # Build INDRA statements from RDF
    bp = BelProcessor(g)
    bp.get_complexes()
    bp.get_activating_subs()
    bp.get_modifications()
    bp.get_dephosphorylations()
    bp.get_activating_mods()
    bp.get_composite_activating_mods()
    bp.get_activity_activity()

    # Print some output about the process
    bp.print_statement_coverage()
    print "\n--- Converted INDRA Statements -------------"
    bp.print_statements()
    return bp

if __name__ == '__main__':
    # Make sure the user passed in an RDF filename
    if len(sys.argv) < 2:
        print "Usage: python bel_api.py file.rdf"
        sys.exit()
    # We take the RDF filename as the argument
    rdf_filename = sys.argv[1]
    bp = process_belrdf(open(rdf_filename).read())

Handle error in RDF when parsing