def _main(input_file_path):
lines = []
with open(input_file_path, 'r') as input_file:
lines = [l.strip() for l in input_file.readlines()]
refs = refparse.parse_cse_refs(lines[1:])
for ref in refs:
print ref
def _main(input_file_path):
lines = []
with open(input_file_path, 'r') as input_file:
lines = [l.strip() for l in input_file.readlines()]
refs = refparse.parse_cse_refs(lines[1:])
for ref in refs:
print ref
def run(self, input_file_path, input_format, levels, search_trials,
perform_layout, output_file_path):
input_file = codecs.open(input_file_path, 'r')
input_lines = input_file.readlines()
input_file.close()
drug_name = input_lines[0].strip()
self.net = litnet.LitNet(drug_name)
self.net.g['method'] = 'topdown'
self.net.g['levels'] = levels
drug_index = self.net.add_v(type='drug', label=drug_name)
if search_trials:
trials = self.ct_client.search(drug_name)
for trial in trials:
trial_index = self.net.add_v(type='clinicaltrial',
title=trial['title'],
label=trial['nctid'])
self.net.g.add_edge(drug_index, trial_index)
refs = trial['biblio']
if refs:
self._add_layer_of_refs(refs, trial_index, levels)
if input_format == 'cse':
fda_index = self.net.add_v(type='clinicaltrial', label='FDA')
self.net.g.add_edge(drug_index, fda_index)
fda_refs = refparse.parse_cse_refs(input_lines[1:])
self._add_layer_of_refs(fda_refs, fda_index, levels)
elif input_format == 'pmid':
refs = [{'pmid': pmid.strip()} for pmid in input_lines[1:]]
self._add_layer_of_refs(refs, drug_index, levels)
if self.verbose:
self._print_counts()
print self.net.ref_counts
if self.verbose:
print 'Postprocessing...',
sys.stdout.flush()
self.net.remove_dup_authors()
self.net.propagate_pubdates()
if self.verbose:
print 'done.'
if perform_layout:
if self.verbose:
print 'Performing layout...',
sys.stdout.flush()
self.net.layout()
if self.verbose:
print 'done.'
if self.verbose:
print 'Saving...',
sys.stdout.flush()
self.net.save(output_file_path)
if self.verbose:
print 'done.'
