def load_pmcid(pmc_id):
# pmc_id = 'PMC3031885'
current_directory = dirname(abspath(__file__))
xml_text = pmc_helper.get_pmc_full_text_xml(pmc_id)
print "got PMC XML"
fries_json = reach_helper.process_nxml(xml_text, 'fries')
json_file_path = join(current_directory, "test-files", pmc_id + ".fries.json")
with codecs.open(json_file_path,'w',encoding='utf8') as f:
json.dump(fries_json, f)
output_file_path = join(current_directory, "cx_output", pmc_id + ".bel.cx")
out = open(output_file_path, "w")
cx = reach_cx.ReachCX(out)
cx.fries_to_cx(fries_json,{
'type' : 'pmid',
'uri' : None,
'title' : "fake title",
'contributors' : [],
'identifier' : '12729465',
'description' : ""
})
out.close()
ndex = nc.Ndex(host='http://dev2.ndexbio.org', username='******', password='******')
cx_stream = open(output_file_path, 'rb')
print "Saving to NDEx"
ndex_uuid = ndex.save_cx_stream_as_new_network(cx_stream)
print "Done Saving to NDEx"
return ndex_uuid
import pmc_helper
import reach_cx
from os import listdir, makedirs
from os.path import isfile, isdir, join, abspath, dirname, exists, basename, splitext
import codecs
import json
import ndex.client as nc
pmc_id = 'PMC3031885'
current_directory = dirname(abspath(__file__))
xml_text = pmc_helper.get_pmc_full_text_xml(pmc_id)
print "got PMC XML"
fries_json = reach_helper.process_nxml(xml_text, 'fries')
json_file_path = join(current_directory, "test-files", pmc_id + ".fries.json")
with codecs.open(json_file_path,'w',encoding='utf8') as f:
json.dump(fries_json, f)
output_file_path = join(current_directory, "cx_output", pmc_id + ".bel.cx")
out = open(output_file_path, "w")
cx = reach_cx.ReachCX(out)
cx.fries_to_cx(fries_json,{
'type' : 'pmid',
'uri' : None,